Installing the Fuel Pump:
I had too many pictures for this one post so instead of posting them all in this thread, here is a link to my DIY fuel pump install:
https://www.audizine.com/forum/showt...l-Pump-Install
The 01E 6-Speed Swap and Clutch and Flywheel Upgrade:
I originally was planning on keeping my stock 01A transmission and rebuilding it, but I had a friend offer me a trade for some drivetrain parts so I ended up going down the 01E swap route. I wanted a 6-speed and the higher top speed (hopefully) and this transmission should be plenty strong to handle any kind of power this car will make.
Here is the list of parts you will need for this swap:
-01E 6-speed transmission from a B5 S4. A C5 A6 01E should work fine too, but if you get an 01E from any Allroad you will have shorter gearing (4.375 final drive instead of 4.11) and transmission cooling lines you will have to find something to do with. It can still work, but just be cautious of those 2 things.
-01E transmission mount brackets (the bracket that bolts to the transmission housing).
-01E shift linkage: You will need the 2 long shift rods and the crossover rod. I got the entire shifter assembly with rods, shifter, shifter box/housing, knob and everything with mine so I will be using all of that. You will want an 01E shifter, but you should be able to reuse the shift box/housing, shift boot and either knob. I am replacing all the shifter components though.
-01E B5 S4 manual front axles.
-01E B5 S4 manual driveshaft.
-01E B5 S4 manual rear diff. If you choose to keep your stock rear axles, you will want to swap your rear diff axle flanges from your A4 diff onto your S4 diff. The inner flange on the cv axle is different on the S4 and A4. So your 2 options are to either swap the S4 rear diff with S4 axles, or swap the S4 diff with A4 axle flanges in the diff and then reuse your rear axles (this is what I did). An 01E rear diff from and A6 or Allroad will not work.
-Clutch options: The kind of clutch setup you go with will determine what bell housing spacer you use. A lot of people are confused on whether that spacer goes with the engine or transmission... That bell housing spacer goes with the clutch setup you use, on any Audi. The input shaft protrusion on all Audi manual transmissions is the same, and the spacing between the crankshaft and the back of the block is the same on similar engines (from example a 1.8 vs a 2.0, or a 2.8 vs a 2.7 vs a 3.0). So this means that you want to use the bell housing spacer from whichever model Audi you're using the clutch from. I'm choosing to go with a 2.7 TTV single mass steel flywheel specifically setup for a B7 RS4 clutch (I'll be using a stock B7 RS4 clutch, this setup should be able to hold 350 tq no problem). All in all this is a 2.7 B5 S4 setup, so I will be using a 2.7 bell housing spacer. The 2.7 and 2.8 have the same crankshaft (even the 3.0 has the same rear crankshaft flange) so you can use any flywheel and clutch you want between these 3 motors. I could have kept my stock 2.8 clutch setup or upgraded to an aftermarket 2.8 clutch if I wanted to. My flywheel and clutch cost me $590 and it will feel like a stock clutch yet hold a pretty good amount of torque. It's probably the cheapest setup you can find that's still quality and I don't think I could get a 2.8 flywheel and clutch on this same level. One last thing to keep in mind is if you're keeping your stock A4 or 2.8 transmission and you go with a 2.7 clutch and bell housing spacer, your transmission will be moved 11 mm further back because of the spacer so you will want your engine and trans sitting as far forward in the mounts so that the driveshaft has enough room. Also if you're using an 01E trans with a 2.8 or 1.8 clutch setup, you will not have that bell housing spacer so that transmission will be sitting 11mm further forward. In this case try and set the engine and trans as far back as you can to fill in that gap where the driveshaft mounts. I will be using a 2.7 clutch, trans, and driveshaft so everything should line up exactly as it should.
-There's minimal wiring modifications you need to make if you're swapping from manual 5-speed to manual 6-speed. The crank position sensor is the same, and the wheel speed sensor is the same. The reverse light switch is the only thing that’s different and the only thing you’ll have to rewire. The cool part about it is the wire colors are the same on both a 5-speed and a 6-speed. So just make sure you have the connector pigtail for an 01E, and just cut the connector off the end of the 01A harness and solder the two wires to the new 01E connector. The wire colors are the same so you’re simply just attaching the 01E connector to the end of the 01A harness in place of the old connector.
For my swap I decided to rebuild every single drivetrain part just because I want this to last a long time. I'll explain how I rebuilt everything in detail, except the trans since JHM has a very detailed video on the 01E rebuild already.
Rebuilding the rear diff:
This is just a shaft seal rebuild, I did not modify the differential or replace any gears or bearings.
This DIY is assuming you have the differential out of the car and the fluid is drained. You can technically change all these seal with the diff in the car, but if you're changing all 3 I would recommend pulling the diff. If you're just replacing the pinion seal on the driveshaft side, keep the diff in the car, it's actually really easy to change without pulling the diff if need be.
I started by replacing the 2 axle flange seals. The axle flange cups can be removed with a 6mm allen or hex key. It’s just that one bolt in the middle that holds them. You can use an impact hammer or thread two axle flange bolts in and block them with a breaker bar or something to keep the flange from spinning while you loosen the bolt.

Pull the axle flange out and the seal is right there. Pull the seal out, it shouldn't be too tight, you can either use a slide hammer and pull on the lip of it or pry it out with a flat head screw driver. Install the new seal and make sure it is seated evenly the whole way around, you don't want it crooked. On one side of the diff you can hammer the seal all the way in until it seats against a machined lip in the diff that will seat it perfectly, but on the other side if you hit the seal too far in it can fall into the diff. On this side you want to work very slowly and make sure that it's seated right when you're finished tapping it. It should be recessed about 8-10mm from the outside edge of the diff housing.

Once the seal is installed, bolt the axle flange back on and torque that 6mm allen bolt to 18 ft-lb. Now those two seals are done.
The pinion seal requires you to pull the front half of the diff housing off. Unbolt the four 8mm allen bolts that hold these two housing pieces together.

Pull the long skinny part of the housing off and there is a coupler that will have either stayed on the bigger diff side (in which case you don't have to do anything) or it will have stayed on the splined shaft that's on the long skinny side (most likely). In this case use a small 2 jaw gear puller to pull the coupler off the splined shaft.

Now you'll want to remove the plug on the end of that diff housing piece near the driveshaft flange. Remove the snap ring that secures it and thread an M8x1.25 bolt into the plastic plug (a driveshaft flange bolt works fine) and use it to pull the plug out.

Now you can see inside the housing and on the end of the shaft there’s a snap ring in there that has to be removed. This is a tricky one and you'll definitely want a decent set of snap ring pliers to get at it. Unlock it and just move it up the shaft a little bit. It will be slid all the way off the end of the shaft as the shaft gets pressed out.

Once that snap ring is unlocked, set up your diff housing in your press like this and press the shaft out the end of it to remove it. Catch that snap ring when the shaft is fully removed.

You'll notice that I have my bearing press sitting on an 8" steel pipe while I'm pressing the shaft out. I bought that 8" diameter x 12" depth pipe for rebuilding transmissions and diffs and it comes in real handy if you're pressing large items that can't fit between the gap on the shelf of your press. Depending on the type of press you have, you can probably do this step without it, but if you use your press to rebuild a ton of stuff like transmission etc. I'd recommend getting a similar size pipe. I think I paid like $16 from a pipe yard for mine.
Anyway now you can finally replace the seal on the end of the diff housing. Be careful when installing the new seal because it's really tight and this seal can bend easily if it's not installed straight. I also like to use transmission assembly lube on the new seals and around that spring to keep the spring from falling out when hammering the seal back in.

When you're reinstalling the shaft, put the snap ring on the end of it before you slide it in so that the snap ring slides all the way back down the shaft so that you can re-lock it. Pressing the shaft back into the housing is easier than removing it on the press. Reinstall everything and torque those 8mm allen bolts to 33 ft-lb.
Another thing I did is make some poor-man upgraded diff mounts. I filled all my stock rubber mounts with 3M black window weld. I had a lot of diff slop before so I'm interested to see how these work for a little $25 upgrade.
I believe the rear diff takes about 1.9 liters of fluid. I like to use the genuine Audi gear oil.
Torque specs:
Rear cross member to frame M12 bolts: 70 ft-lb
Rear cross member to diff 8mm allen bolts: 33 ft-lb
Front mount to diff 8mm allen bolts: 33 ft-lb
Front mount crossmember to chassis T50 torx bolts: 30 ft-lb. T45 torx bolts: 17 ft-lb.
The Transmission:
Since JHM has a really good video on rebuilding an 01E, I'm going to save a few pages of this thread by not writing a DIY, but I'll explain what I did and will put a few pictures up. After fully disassembling this trans I found that it's in really good shape. The 1-2 collar looks like it's brand new, I've never seen an OEM one this good. So all I did was replace the synchros with some spare OEM Audi ones that I have that are in a little bit better shape. I also replaced the brass 4th gear syncrho with an OEM Moly-coated one. I replaced every shaft seal on the transmissions so I won't have to worry about leaks for a while. I also am modifying the center diff to be a 55:45 rear split. There's 2 teflon-coated washers that get replaced with steel ones to make it 60:40, but no one on the forums sell these washers anymore so I was only able to get ahold of one washer to replace. This will make the diff a 3:1 55:45 split which will still be fun. Here's some pics of the process, I painted the parts of the transmission housing that were rusting and nasty-looking.
As far as rebuilding the front axles, I just replaced the boots and re-greased them. The process isn't too tricky, it's just messy as hell. There's a lot of write ups out there, but you just remove the snap rings on the inner flanges, pull the cv joint off, clean and replace the boot, put everything back together. For the outer boots there’s no snap ring so you just set the joint on the press, use an extension or something to push the shaft out through the axle bolt threaded hole and then you can replace the boot and press the joint back on.
Rebuilding the Driveshaft:
I can only put so many pictures in this thread so here is the link to my DIY Driveshaft rebuild thread. Pretty much I replaced the center u-joint and support bearing and freshened up the CVs.
https://www.audizine.com/forum/showt...eshaft-Rebuild
Custom 2.8 Downpipes:
This ended up being a ton of work and I’m not sure if it was really worth it, but at least now I can say I have a set of custom 2.5” 2.8 downpipes lol. I started with XS-Power B6 3.0 downpipes.
https://www.ebay.com/itm/XJHMS-B6-A4...xI8C:rk:2:pf:0
The bolt pattern on the flange has a 12 mm greater diameter so first you have to re-drill the bolt pattern to be smaller. Each bolt hole has to move 6 mm closer to the center. The flange is really, really hard steel so it will take forever to redrill the pattern. The way I see it, there’s two ways to do this. The way I should have done is cutting the flanges off, redrilling the pattern on a drill press, and then welding the flanges back on. The way I did it is using a 5/16” hole saw bit,
https://www.homedepot.com/p/Milwauke...0507/204994401. I submerged the downpipe flange in about an inch or so of water so I’d be drilling the hole underwater the whole time and that way I wouldn’t worry about it overheating and trashing the bit. I was able to use that bit throughout the whole process without burning it doing it like this, and then I just used a standard 5/16” bit to clean up the holes when I was done. It definitely took a few hours to do this.



If you’re like me and you don’t have a pipe bender, the next step is to cut each downpipe into 3 sections.

Bolt the first section to the manifold and try to guess the change of angle it needs. Then cut out an angled piece of pipe, line it up with the new piece of pipe, mark it with a sharpie, pull it out and tack weld it (I didn’t have enough room to tack weld it in the car since it was on jack stands). Then reinstall it on the manifold and see if it fits. If so then you move onto the next section and do the same thing, if it doesn’t fit then you cut the tack welds and try again. I had to keep going in and out of the car, bolting and unbolting the downpipe to tack weld it and hope I welded it at the right angle since I was just guessing. You’ll want to do this part with everything installed in the car besides the axles. I first starting making the downpipes with the engine and trans outside the car and when I put it in they didn’t fit. So do all of this work with everything installed. I also used a 4 ft section of spare 2.5” exhaust pipe to make these.


The passenger downpipe on a B5 is about 6” longer than a B6 downpipe and the driver side is about 2 ft longer so you’ll have to add that much pipe to the custom downpipes to get them to reach the catback. I had the catback installed in the car and then measured the amount of extra pipe I needed and tacked it under the car. I was using my stock catback so I reduced my downpipes to stock size. If you do this you’ll want to clamp your reducers to the catback and then tack everything so that when it’s welded it’ll line write up where it needs to. In the end I cut and welded each pipe in about 10 different places... the whole project took about 40 dreadful hours.


I then ceramic coated the downpipes to hopefully make them last longer without corroding.
Other things I did:
I added an AEM Wideband AFR Gauge and a Glowshift boost gauge to the car. For the Wideband gauge I added an O2 sensor bung to the driver side downpipe right at the bottom of the downward section next to the transmission. The wiring harness they give you is pretty plug and play. I ran it behind some heatshields in the transmission tunnel and up through a hole I drilled in the ECU box and into the interior. The harness connects from the O2 sensor bung to the gauge, and then from the gauge there’s another harness that just needs to be tapped into 12V ignition controlled power and ground. For the boost gauge I ran the boost hose from a T that’s tapped into the vacuum hose coming off the fuel pressure regulator. This hose always has manifold pressure so it’s the one you want to use. I also ran this through the hole in the ECU box and then sealed the hole. For the boost gauge I tapped one wire to constant 12V, one wire into ignition controlled 12V, one wire into the headlight fuse, and one wire to a ground. I tapped all the power supply wires for my gauges using add-a-fuse kits. The boost gauge pod I bought is made by a dude on eBay and they sit in the driver side defroster vent on the dash.
https://www.ebay.com/itm/B5-model-A4....c100005.m1851
I really like having the gauges there. I just cut a hole in the air duct below the defroster vent to run all the wires through.
Another thing I did was replace the old brittle PCV hoses with silicone ones. I ordered 5/8” ID silicone hose from eBay:
https://www.ebay.com/itm/5-8-ID-Flex...S!-1:rk:1:pf:0
You order it by the foot and I got 6 ft. I cut the plastic hoses off all the plastic connectors and elbows and then you pretty much just attach the silicone hose to the stock connectors and elbows. The 5/8” fits perfectly and it’s pretty snug so you probably don’t need hose clamps, but I installed some anyway.
I also swapped out a lot of random interior parts including my dash… Believe me a dash is something you’ll never want to have to take out lol
I also repaired part of my front frame rail that was warped from some previous crash before I bought the car. I cut out a section of good frame rail from my parts car a while back, measured mine, cut it, lined up the new piece and just welded it. It lines up to the core support almost perfect now and my front end actually fits haha
And that pretty much covers the majority of the DIY stuff I did for this build. Anything extra I do will be added throughout the thread, but hopefully these first couple posts are enough to start you off in the right direction. As always feel free to ask any questions.
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