No boots. The problems comes with mud and sand, otherwise it's just a personal choice not to run them.
You will be happy with the 12s. I have 14s in the back but the mounting is far from stock LOL.
What is your concern about the front driveshaft? I have (what I think are) 1350 CV with 1350 at the axle on the front. IIRC it's the non-coated big slip/spline, like 7 or 8". I don't bind the U-joints at full droop. The slip is plenty long. I have my axle moved forward about 2", run ORD 52s, about 5" lift AND the T-case is clocked flat. Lots of angles but it's been good so far.