The non-factory front u-joint if you want call it that drives me nuts. I'd have a driveshaft made Using OP's front yoke or a new one. Have 1350 u-joint at both ends and use combination u-joints if needed to mate both ends.
I see what you are referring to. Those shims were set correctly on the pins. I just have them sitting like that cause I took a photo. I did try to reverse them and I still had a vibration. I tried with 2 degree shims and the 4 degrees both ways cause I did think I was confusing myself. I am considering swapping back to my longer slip yolk and having the big yolk installed on the driveshaft.Just looked at this thread. In your initial pictures (post #1) the 4th picture shows you have Two 2 degree shims.
First problem is you have them in the wrong position. They need to go in from the front to raise the pinion up to 3.8 degrees.
Second problem is they need to go all the way under the perch not the way you have them installed. I think you are confused with the "pinion up" claim. Your last picture in post 1 shows your pinion arrow up but in fact it is down. I think if you get those shims turned around and in the proper place with the pinion nose up you will see a big improvement.
Another thing I would do is since you have the large yoke on your pinion, I would have a drive shaft builder cut off that small yoke on the driveshaft and put the big one on since that could be causing some of your problems also.