Alright, so as most of you know, the B3 cars in the states had two engine options: the 20v naturally aspirated NG found in the 80s and early 90s, and the 20v naturally aspirated 7A, found in the later 90s and coupes. All B3 cars came with the same transmission and drivetrain. They all had 01A transmissions with 4.11 final gearing. The 01A transmission is closely related to the 01E, which makes the O1E a relatively easy swap. The 01E transmission bolts right up the any 5 cylinder block, so no need for any sort of bell housing adapter or anything like that, other than the bell housing spacer which was installed in the factory on the 01E cars.
Flywheels:
If you have an NG: first off, why the hell are you swapping a 6 speed into an NG? :barf: I believe you can keep your stock flywheel, but you might be the only person to ever attempt this swap.
If you have a 7A: you can keep your flywheel. You can also keep your clutch, or use an upgraded 7A style clutch.
If you have a 3B 20vt swap: your 3b was paired to an 016 transmission, which has its pilots bearing in the crank. The O1A/O1E have their pilots bearings in the flywheel. You cannot use an NG flywheel unless you insert a timing pin. A 7A flywheel and clutch fits the 3b, has a timing pin, and has the pilot bearing in the flywheel, so 7A flyhweel/clutch is a good solution.
If you have an AAN swapped into your B3, the AAN already had an 01E, so the AAN flywheel/clutch will work just fine.
Axles
The axle cups are the part which spline into the transmission, which you physically bolt the axles to, shown here:

Audi used 2 different size internal splines on their transmissions, as well as two different sized axles. The large spline is a little over 29mm, the small size is a bit smaller(I didn't measure). The large axle size, seen here, is 108mm:

The small axle size , seen here, is 100mm:

The 01A in all the b3 cars uses the small spline with 100mm axles. The 01E uses large spline and 108mm axles, meaning the transmission will not bolt up as-is to the smaller axles in a B3 car. Luckily, the 4000 quattro used an 016 transmission, which uses large splines, and the car itself was fitted with 100mm axles. You need these axle cups if you want to use an 01E with your stock axles.
(I believe the B3 cars also use this size cup on the right rear of the differential, so if you have a couple spare B3 diffs, you can use those)
As you can see here I have the 01E axle cup comparing it to the axle cup from the 4000q.
Same internal spline size:

Different axle sizes:

These fit with no modification into the 01E, but keep in mind you need the bolts from the 4k! The bolts are not the same, you cannot use the bolt from the 6 speed, and the 01As don't have any bolts, so be sure to keep the bolts from the 4k! You can see the differences here:

The 6 speed bolt is the shorter, square shoulder bolt. If you try to use the 6 speed axle cup bolt with a 4k axle cup, you won't even make it out the back of the axle cup, shown here:

In case you need to source a similar bolt:

Driveshafts:
The 01E is physically longer than the 01A by about 1 inch. This means your driveshaft is too long as is. Luckily, the same 4KQ you got your axle flanges from has a driveshaft that just so happens to be 1 inch shorter, and bolts right up! :woowoo:
Here is an 01A driveshaft next to a 4K driveshaft:


Transmission
It's worth mentioning that the UrS cars came with an 01E, but it was a 5 speed. People can and do swap those into B3 cars, but this post is specificlly about the 6 speed version which was found in a few cars. People mostly associate the 6 speed 01E with the b5 S4, but it was also found in the C5 A6 manual, as well as the C5 allroad. Unfortunately, the allroad does NOT have 4.11 front final drive, so you cannot use it as-is in your B3. The 6 speed 01E was also used in the RS2, but those are hard to find and quite expensive, so chances are good you'll be looking for eiher a B5 S4, or a C5 A6 2.7t. I found mine in a local picknpull. It cost $99 plus a $30 core, with a 30 day warranty.
Here is an 01E(top) next to an 01A(bottom):

Note the 01E uses a stabilizer bar which bolts to the floating shifter assembly in a B5/C5. I won't be using this, so it's simply removed and discarded.
You can see the transmission shift levers have very similar "shifter ends," (and by that I mean the part of the lever that bolts to your shifter, as opposed to the part that bolts to the transmission) but the 01E has a "cupped end" which is concave down, whereas the 01A that cam out of your car is concave up, shown here:

You may have read about "cup flipping," this is what they are referring to. The end of the 01E shift lever is cut off, and rotated 180 degrees to allow it to be bolted up to your stock shifter assembly. I have normally used the 01E shifter assembly and modified it to fit in my car, but I'm trying the cup flipping for the first time here.
When you cut the shaft, you should be aware that the tube is hollow, and completely filled with about a pound of buckshot, or something similar. It's purpose is to add weight to the shaft to improve shifter feel, similar to a weighted shift lever. If you're using an angle grinder, wear safety glasses or a face shield, and be sure that your shaft is positioned in a way that the buck shot doesn't all come falling out, hitting the grinder, and shooting red hot buck shot straight into your eyeballs.
Here's a picture of the weight.

Now I was told the end simply gets cut off and flipped 180 degrees, which is what I did first, and here is where I cut.

However, when I tacked it up and compared it to my 01A, I found that the cupped end angled up towards the ceiling by about 30 degrees. This may or may not have worked, but I wanted it to more closely resemble the 01A, which was fairly parallel to the floor. I end up bending it down to match, but did not change the clocking of the cup end. This is what I ended up with:


As you can tell they look quite similar, but I'll be sure to update how it all fits in the car.
After you've swapped axle cups and modified the shift lever, the transmission is ready to install.
Mounts
You'll need new mounts, neither the 01E mounts nor the 01A mounts will work. You can use OEM RS2 mounts, but they are quite hard to find and quite expensive. Luckily, a number of people now sell replica RS2 transmission mounts. Keep in mind the RS2 was a b4, not a b3, which means it had a different subframe. If you want to use RS2 mounts on a b3, you need to use 40mm spacers on one mount, other than that, they are a direct fit. I will be making my own mounts, because I don't want to spend $300. I'll post pics of the mounts as I make them. That's as far as I've gotten, I'll be posting more as I make progress. Hopefully this will be helpful to someone someday!
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