When I was in Moab last year, I ran with another Tracker that had stock 8v and an automatic. He was running 33's with lots of wheel well trimming and 5.13 gears. Our automatic's worked great. You do not have to slip the clutch to creep through the rough/hard sections, and if you run bigger tires going to 5.13 gears is a big reduction. Finding lower gears for manuals is hard to do.
On the rear end, swap the third member, not whole rear end. The 4 door has bigger brakes that you want to keep. The front you can just swap the whole differential assembly.
It may be easier to swap out all the front wiring (motor, dash, engine compartment), rather than converting it.
If you proceed, post up in the Build Diaries, How-To, DIY instead of working in two different sections.