C5 A6 2.7T 6speed - Stutter/Hesitation at moderate acceleration

[Leipzig]

First post please forgive any grievous errors in forum policy.

My daily driver is a 2000 C5 A6 2.7T Quattro 6speed. I’ve got a 98 e36 M3 sedan 5speed as a weekend warrior.
The A6 is an excellent machine that has performed more or less flawlessly for.... a very long time. Current mileage is just under 154,000.
2 months ago I started running into a random no-start condition where the engine would not turn over. Along with the no-start the car threw a ton of codes involved with the o2 sensors, cats, engine bank 1, and most importantly, pc rom error. It was time to change the o2 sensors, after that, the catalytic codes vanished.. but bank 1 and pc rom remained, as did the failure for the car to start at seemingly random times. I managed to find a salvage ECU from a 30,000 mile C5 2.7t ’00 6speed on Ebay for 130 bucks. Plugged it in… boom. All codes fell by the wayside.

BUT….

Since those repairs, the car hesitates/surges/stutters (hard to explain) at various points in the power band while accelerating. It’s a minor flutter that I feel. If I accelerate slowly, I don’t feel it. If I gun it, I don’t feel it. It’s really only during moderate acceleration that I feel the engine shudder, and it’s usually between 2 – 3k rpm (not sustained during that range, just at random points). The car is not throwing any codes, no engine lights, no blinking anything. Drove it for 2 days after the repairs (150 miles) and plugged it into a dealership system… no codes. I disconnected the battery for an hour to reset the ECU, idled rough for a moment, then smoothed out… but once I got the wheels rolling, same issue under moderate acceleration.

So I’m left wondering if any of the repairs that were made could result in these symptoms or if randomly something else went awry the moment the other issues were fixed.
-could the ECU need to be reprogrammed (this puppy was plug and play, fired the car right up, identical model number to the old ECU, amazingly easy)
-could one of the new o2 sensors be bad and the car is running rich/lean?

Those... seem doubtful.

-could the throttle body boot have failed?
-do these symptoms indicate a leak in the forced induction system?
-diverter valve?
-spark plugs?
……..... maybe?

If I rev the car in neutral, it’s as smooth as my ass in 82’. I don’t think it’s a misfire considering there are no codes being thrown, and it only happens when moderately accelerating under load. Seems like a turbo issue, like they aren’t holding pressure… or something. I visualize in my head the throttle body boot having a minor tear in it, and as boost pressure builds, the tear starts to open up and pressure to the engine suddenly starts to fluctuate. I don’t see the needle on my tack jump around a lot when this happens… I just feel a relatively minor stutter/flutter/hesitation in the engine - that definitely did not exist prior to the recent work.

Sorry for the drawn out explanation… hoping the Audi community can drop some knowledge.

Thoughts? Where should I begin?

[Leipzig]

...

[LINDW4LL]

Hello! It's hard to say whether or not it appearing after the other repairs were done was a coincidence or not. I certainly wouldn't expect the ECU to cause it unless it had a [poorly done] modified tune of some sort.

When was the last time your plugs were changed? That would be an easy thing to start with. Second, you could have a boost leak I suppose- torn TBBs and DVs are quite common at higher mileage, but I'd think you would notice that at heavier throttle, too. You can try logging Requested Boost vs Actual Boost with Me7Logger if you have a VagCom cable.

[Leipzig]

Timing belt was done 40,000 miles ago, along with with spark plugs. Seems the plugs are due for replacement (inexpensive, i will replace), but i just can't imagine they are the root of this issue considering the sensation i feel is relatively limited to specific driving conditions. It really does not feel like a misfire, which it seems the ECU would definitely throw a code for... I took a look at the TBB and the DVs this evening. I felt all around the TBB (hard to really examine the bottom) and did not see any evidence of failure (tear, hole, etc)... but the hose between the DVs, was slightly frayed/potentially damaged.

I read about trying to locate vacuum leaks with a toilet paper roll held against your ear to really "pin point" a "hissing" sound while the motor idles. (apparently that could be evidence of leak).... anyway, i definitely hear a focused hissing noise in the vicinity of the DVs... shit, it could be anything. Figure I need to disconnect the TBB and look for cracks. Bunch of Hocus Pocus car diagnostic will get me nowhere.

Wish the car would throw a code/a dog a bone.
smooth operator, won't show it's weakness.

Probably need to invest in a Vag

[glennda5id]

If you had a vacuum leak you long term fuel trims at idle will be off. Do you have VCDS? You could have mis fires logged that aren't at the threshold to throw a code.

[Leipzig]

I do not have VCDS, but my mechanic would be able to access the logs.
What are your thoughts on putting some decent miles on the car... I've got a 5 hour drive to make this weekend.

[glennda5id]

I suspect you have a minor issue that will be difficult to diagnose now. It will most likely get worse and then be easier to diagnose. My advice would be to drive it until it gets worse.

[HoboWithApricot]

Not sure if you figured this out already, but I thought I'd toss in my .02. I have the same year car, 2000 a6 2.7t. When I bought the car it had a pretty violent buck whenever I gave it any kind of gas. I could slowly accelerate and it would be smooth as can be. The minute I gave a little extra throttle it'd shake and feel horrible. I replaced my spark plugs with the ngk platinum factory plugs (I think they were like $9 a piece on amazon) and the problem went away immediately. Whoever had it before me put champions in and they were completely hatched. I'm surprised it ran at all. Best of luck figuring out your issue! Hopefully this helps