Agree about not having any warpage being not very realistic, but it can be done with minimal warpage and yes, the alignment should be checked after. Alot of guys will use an alignment bar when mocking the balls back into the housing to keep it all axially straight, but I'm sure alot of guys just go for it with decent results. there is not alot of slop between the balls and sockets, so they will be within a certain window of true without a bar... you can in effect add up your shim angle and just transfer that to your caster angle. if you're running 6* of shim at 3* caster angle and your pinion angle is within spec, roll your balls and spring pads back 6*. if you're at 6* of shim and your caster is 1* and your pinion is set, roll the balls and pads back 8*...
cut your balls loose, cut the pads loose, point the pinion where it needs to be (dead on at the tcase flange with double cardan type shaft; parallel to the Tcase flange if not cardan), bolt the housing to the springs and put the weight on the housing. adjust pinion angle again if needed. tack the spring pads temporarily. roll the balls back to achieve 1-3* caster depending on your tire size/lift...
welding the housing will warp it. this can be minimized by preheating and post heating the areas that will be getting hot, and by rotating your way around the bead- not just a long steady burn, but and inch here- and an inch 180* away until it's full circle. taking several passes lessens the amount of acute heat applied at any one spot at a time. I went with 3 passes on my fzj80 rear when I narrowed it. I used a 120 volt mig. I used a deep V groove and valley welded the first pass. the second 2 were overlapping each other, kind of side by side, over the top of the first pass. I prolly have 25K hard all kinds of miles on that axle with NO ODD wear on my mud meats with less than the correct number of tire rotations...