I fried my ignition coil harness section of my engine harness, and figured the most cost efficient route would be to swap in a complete harness. But the ones I found that were in my price range were for an auto. Figuring the manual and auto harness could not differ that much I picked it up. The only differences between the 2 harnesses is the auto manual has 2 extra connectors that the manual does not have (not quite sure what they are for) and is missing the reverse light switch that hooks up to the transmission. With some help from walky_talky20, figured how I should go about it. There are a couple ways you can go about it, but this was just cleaner to me.
Assuming you have your old manual harness still, you will be removing the reverse light switch connector and wiring all the way back to the terminals they sit in. If you do not have this, you can follow walky_talky20's write up and simply mock up your own light switch connector with wiring. It is explained in the DIY below for a different scenario when wanting reverse lights.
http://www.audizine.com/forum/showth...a-5-speed-swap
You basically open up the sheathing of the old harness, making sure not to cut into the wires. Underneath that sheathing, the wires are bundled in periodic lengths for stability by tape. Just unwrap the tape. The reverse light switch connector has the pig tails ending at 2 of those little colored connectors that sit behind the ECU in the weather box. One goes to the tan colored one and the other goes to the red/orange 2 piece one.

To remove the terminals from the connector, you need to slide back the little locking tab on the connector (you will see it if you look at it, can't miss them). Then you simply use 2 unfolded paper clips to release the metal terminal end from the connector and pull back. If you look at the connector, you can see where the paper clips should be placed. Below is a pic for demonstration on just a random one (have it being white here makes no difference. it is just for demonstration). These should come out easily, so don't place too much muscle on them trying to force them out. If you do, you will bend the metal clips on them and make them even harder to get out. What I do is push them forward a bit in case they are hung up on the plastic of the connector, then pull back.

-On the tan connector, you want to remove the wire from terminal 5. The wire will be blue/black.
-On the red/orange connector, you want to remove the wire from terminal 1 on the "red" portion of the connector. On this connector, you actually need to separate the 2 halves before sliding back the safety locking tab. The wire will be blue/brown
After you take that out, wrap it in your tape of choice (I used cloth tape) to make a harness out of it.

Place it where it is supposed to go on the transmission. For routing, I used the same hole in the rubber grommet on my false firewall that many run their boost gauge line from. If you don't know what I am referring to, I am stealing this pic from a different DIY.

Earlier I told you about 2 connectors not being used. Well, one of them comes directly out of the ECU box by the rubber seal on the engine harness. Perfect. Just cut that sucker off (leave it in tact if you want to keep the harness as one full unit though. at this point, you would probably find it easiest to remove the connector and push the cable back into the weather box). Now, we have an easy access port into the ECU box. Snake the harness' cable you made for the reverse light switch into there, and now all you need to do is wire them up. They go right back into where they came from from your old harness.
*On one of the connectors (can't recall which one), the terminal you need is being occupied. Just remove that wire from the connector (pig tail also) with the paper clip method mentioned before and place your reverse light switch wire in there. But be sure to wrap that pig tail being removed with electrical tape. That wire is going to the other connector not being used (have no idea what it is for) and poses no threat removed.
Enjoy having reverse lights!
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