The pinion angle is going to want to land in a sweet spot between parallel pinion & t-case output angles and caster, without doing exactly as you've mentioned: cutting & re-clocking your axles "C's".
This driveshaft angle is what makes high pinion axles sought after for these swaps.
I did not clock my axle C's, though I did use some (maybe) 2.5deg shims under the front leafs to get my pinion higher with minimum affect on my caster. WIth that said, I do not have excessive driveline vibration when in 4wd, but I also do not do highway speeds in 4wd.
Here's some good background information regarding pinion angles & u-joints:
Driveshaft Angle Explained This video will demonstrate the proper angles for a drive shaft in a stock Jeep or Truck and how the rules change when you add a suspension lift. The video below demonstrates what is happening to the shaft at different angles, how improper angles can cause speed...
4xshaft.com
I'll add that if you get a custom shaft with CV joints on either end, then none of these angles will matter. You'll have smooth operation at any angle or speed of operation