Not too much of a surprise.
Sounds to me like you either need to grind the yokes a little, look at a cut-n-turn (best solution) or look into something like Tom wood's offset u-joints (which will vibrate like heck, but solve your binding issues).
With the fat-end forward you are pushing the pinion down, making your joint angle worse, but at the same time they are countering the negative caster the extended shackles are creating, and probably adding a degree or two of positive caster which will help handling and tracking.
I think I've also noticed a difference in pinion and drive-shaft yokes which would be why some people have issues and others don't. Some yokes have more meat and offer less angularity than others. If you feel comfortable you can clearance the yokes and see if that helps, or dial back the shims.
Another thing, especially if everything is new, is to make sure the bolts aren't too tight, then drive it around a bit on various terrain to "break in" the springs a bit. They most likely will soften up a bit and settle into their "natural" arch. They might be a little stiff right now and artificially lifting the truck up higher than "normal".
Also make sure nothing sticks out to you being out of place. Like chris mentions, make sure the motor and tranny mounts are where they should be, nothings tweaked or been spaced off strangely....
Just some ideas to try and/or explore.