What kind of trails do you hope to run? It sounds like things of the Kane Creek ilk are really the limit you intend to go, in which case I wouldn't bother with the 35's. 35's are nice, and I liked the way my last couple ZJ's worked with 35's, 4.56's, 5" lift and long arms but I wanted to be able to run trails up to the level of Pritchet. 33's vs. 35's do make a difference on a trail like that. Otherwise, with your already undersized running gear, I would err on the side of safety and run the smaller tires that are overall easier on your drivetrain. Remember, on d30's and d44's, it's not just the shaft /joint size that you have to worry about. It's the added weight and force of the larger tires being harder on ring gears, knuckles, ball joints, steering etc. Tj's and XJ's run 35's on those axles all the time, but they are also running 6 bangers and don't weigh 5500lbs loaded.
I used to put a 35 in the back. I couldn't use the factory J-bolt or the factory provisions, but it fit. I used 2 ratchet straps and it sucked it in there really well and didn't budge. The seat would fit up with low psi in the spare, but my seats were in the garage anyway since I don't like anyone well enough to have them come along...and I was usually loaded to the brim with glamping gear and fuel anyway.
I've always said, that 4.5" and 33's is the limit on a ZJ unless you're prepared to deal with a can of worms. Anything more requires a lengthy list of stuff to do correctly.