The reason UJOR uses the Sterling axles is because they match the metric bolt pattern the '99-up front axles have, and his kits are made for those metric front axles. Plus you get rear disc brakes as well, of the type that actually works properly. But he says it himself that you can keep your van axle with the standard 6.5" BCD and just bolt on a pair of adapters to bring it to the 170mm BCD that matches the front axle. If you use a kingpin D60 front that has the same 6.5" BCD as your current van axle, so no need to swap axles. If you do decide to swap anyways, you're limited to '97-down axles, which won't have disc brakes.
Regarding the driveline angles, I was actually about to ask you last night if you know what your current ones are. Guess you just answered that though. No biggie, vertical angles are easy enough to figure out with a magnetic angle finder, you can pick one up for dirt cheap from Harbor Freight even, and it actually works pretty decent. Horizontal angles would be via basic trig calculation based on length of driveshaft and offset between pinion and transmission or transfer case output shaft. So, how long is your rear driveshaft from u-joint cap to u-joint cap, and how much do you think the pinion is offset to the right with respect to the output shaft? Good news is that as long as pinion and output shaft are parallel, as in pointing straight front and straight back (up and down tilts do not matter for this) then the horizontal U-joint angles are the same at the front and rear U-joints, and that is what you want to be vibration-free. The reason you have vibrations now could be the shaft does indeed need balancing, or you carrier bearing (if one is present) is not in stellar condition, or when the Cummins swap was done the overall drivetrain angle (adjusted via the transmission mount height) wasn't quite right. The angle finder will show if the last one is a problem.
