-The best way to set arms, (so I've been told) is with the springs removed, bring the axle to full bump and make sure the axle is dead centered. Install the arms, and thats the ideal length ( lowers).
However I believe this is all highly unnecessary, the lengths mentioned in your instructions should be fine . It is a good idea to measure each side of the axle to the first bolt on the T-Case skid to make sure the front axle is perfectly straight (just in case) this could cause some vibes.
-Pinion angle, the yoke should be pointing towards the output on your T-Case, I have found that close is good enough for everything I have done.
- I have ran with caster way out, 3" of lift on stock arms for a while with no noticeable effect on handling.
Do you have an sye?