I guess it's just one of those things when you are hand-building or modifying a vehile that you want to figure out before you weld and bolt everything in, but in your case Cat, I can't imagine your driveline being in a very steep angle, so I wouldn't get an ulcer over it.
As long as you get both of your driveline's ends parallel, level, and both in line, (and you replace both u-joints just to be safe), you should be fine.
You don't have any leaking out your pinion seal or your transmission rear seal do you?
If you haven't checked them, you might want to, because the vibration might have screwed them up a bit.
The pinion seal takes a bit of muscle to break that darn center nut loose to remove the pinion yoke, but both seals are pretty cheap-n-easy to find at a parts store and replace.
I made my own universal tool for pulling pinions out by using a 5 ft junk piece of 4 inch wide X 1/2 inch thick flat stock. I drilled a big hole in both ends, and drilled holes around that to match most Import and most standard Chevy u-joint's bolt pattern on their pinion yokes.
All you have to do is bolt it to the yoke through the u-bolt holes, stick a socket though the big hole, and brace the other end on the ground to stabilize it. Then you can break the nut loose without stressing the rear end.
To tighten it back up after you replace the seal, you just put the pinion back in and hand-tighten it, switch the bar to the other side of the truck, bolt it back to the pinion yoke, and tighten the nut to the recommended torque spec's.
Here's a pic to show you what I mean:
BTW...I loaned it to a guy that works for a tool rental place in town, he copied it for his boss, and now they rent them out for $40.00 a day...lol