I wouldnt worry about an alignment before or after the shims, they wont effect anything up front.
Both joints need to be as close to each other as possible in angles.
If total shaft angle was 10 degrees, you want each joint to be at 5.
Unlike a CV where you just point the pinion straight (minus 1-2 degrees) and let the CV take all the angle.
The max operating angle of a single joint is around 5-7 degrees. Looks like you are pushing that limit. But I wouldnt recommend more then about a 3 degree shim, else the pinion will come up to much, throwing the difference between the 2 joints to far out of whack.