I did a manual swap on my 02 Golf TDI and everything went perfectly. Everything works (clutch switch, cruise, reverse lights) and no CEL or codes. The only mod on this car is larger nozzle injectors from a manual car.
With that said, I have noticed one odd thing that doesn't make sense to me, so I am asking you guys. When I am accelerating, then I let off the gas while depressing the clutch for a shift, I get a little "bump" or "blip" of RPM before the RPM falls as it should. If I slow down the process so that I exaggerate the amount of time I let off the throttle before depressing the clutch, sometimes I get the bump (though smaller) and sometimes I don't.
One other thing that I noticed that might be significant is a slightly rough idle when warm. Nothing severe or worry-some but just enough to be noticeable.
I had an 01 Jetta TDI that was originally a manual that I am using as a comparison. One other observation that is not a complaint, is that the 02 has a bunch more power than the 01 had, more of an increase than I would expect from +1 injectors.
I am guessing that this may be related to some adaptation that needs to be tweaked, but I don't really know where to start with that. Any ideas?