So everything is going well and I'm putting on miles to break in clutch before tuning. I've checked the angle (by sight) of the driveshaft and it looks very good. I reused the same shims from the donor car for the center carrier bearing mount. Crawl under car today thinking maybe I missed something and the angle was off at either the ds (driveshaft) to trans or ds to rear dif. Both points look as straight as I can get them by visual inspection. I'm not sure how sensitive this angle is. If necessary, I could either devise a tool or find the actual vag alignment too.

The vibration is nothing major but I want everthing as perfect as I can get it. I don't care about the cost, I just want to resolve it. As for other rotating components; I used advanced auto reman front 6mt axles, stock rear rs6 axles, stock driveshaft from the a6 donor I parted (120k miles), repacked ds cv joints with fresh grease and new cv seals. I tried moving the center carrier bearing bracket around a bit to see if I could notice a change and found none. I really didn't notice the vibration before I swapped out the rear dif to the new 3.89:1 dif but mufflers were not attached and now they are.

Things of note that may be relevant:

-I poured stiffer rubber into the three rear dif mount bushings,
-I made no note of the rear axle cv joint position to the rear dif flanges and just installed wherever they lined up at first try, the Bentley manual shows dots on the rear dif flange and ds rear cv joint but I made no note of this either since I was mix and matching different components front different cars,
-although, when I installed the front axles I noticed that they do not spin true (can see a slight wobble in the shaft) I feel absolutely no vibration in the steering wheel.

I am am just looking for the next possible diagnosis step. I was thinking of keeping the rear dif flange stationary while rotating the ds a bolt hole or two. Also, there is a local driveshaft shop I can pull the ds and take it to but I was to,d if the weights have not been removed (don't know where they are weighted for balancing) there is no need. Just really want to get to the bottom of it.