Welcome to the site. I had a 77 CJ7 that I built for rock crawling. I'll try to answer your questions based on my experiences.
1. rear end - As long as you stay with 33" or smaller tires, the 2 piece axle will be fine. I ran Detroits in both ends of my 77, they really aren't that bad. If you do the rear, loosen and re-torque the axle nuts to 250 ft/lbs. They do work loose with age, and that's what usually causes failures.
2. I believe the part time conversion on the q-track adds a slight overdrive. You might want to do a slightly lower gear (higher numerically), especially if you increase tire size.
3. Rancho is the stiffest suspension I've ever dealt with, you could remove the shortest leaf to soften them some, but I'd replace them. I had great luck with custom springs from Alcan Spring. They aren't cheap at around $800/set. But they are built to your specs.
4. you could probably fit up to 33" with a 2" lift, but if you like the 31s, stick with them.
5. 401s are getting rare and expensive. They were last built in 1978. It might be easier to find a 360 out of a Wagoneer (up to 1991). Any AMC V-8 from 73 and newer will bolt up. Just remember that AMC v-8s are externally balanced, so you need to find one with the matching harmonic balancer and flex plate or you will have a vibration. You can't put a 304 flex plate on a 360 or 401.
I had Howell-EFI on my CJ7 (360 powered), it was great. I hear a lot of good things about the Holley Sniper or FI-Tech systems. All cost about the same.
Bob
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