The u-joint at the transfer case should have no angle on it. That first section of driveshaft from the t-case to the carrier bearing is essentially an extended t-case output. The differential pinion should be pointed up at the CV (or ~2 degrees below it) so there should be basically zero angle on the diff u-joint as well.

The axle tubes are bigger than 3", slightly bigger than the mini trucks. Part of the problem is the weld bead. I don't remember the exact size. Just measure the distance between the ends of your current u-bolts. I would guess 3.25" would work fine for a u-bolt flip.