1) Try to find a set of Jeep CJ 15x7  steel wheels. They have 3.75" backspacing and seem perfect on these rigs. Either that or run a 1" wheel spacer with stock wheels.

2) This is a popular tire size because it gives a good boost in ground clearance without requiring in-depth modifications to all kinds of other stuff. I don't think they'll fit without a lift, but you can try.

3) If you like the way the vehicle rides and handles loads and passengers, there is no reason to change out the springs. Spacers are cheap and get the job done. If you add spacers to OME coils you get around 2.5" lift and should add a set of diff drop brackets to keep the CV axles happy in the long run. Adding manual hubs will also help with this.

4) Trim as required.

5) Gearing- which gears are you referring to? Axle gears or transfer case gears? t-case gears are great if you're into rock crawling and don't like riding your clutch and brakes. They only help with your low-range though. If you get axle gears it helps with your all-around driveability but most people don't feel the need to regear with 29" tires.

If you do a spacer lift, you can run longer shocks or shock extensions in the back. I believe shocks from a 1991 Ford Crown Victoria are what you want. Doesn't matter  if it's a police model or not, but I'd guess the police model had better valving than the senior citizen model.

In the front, you can put a strut mount spacer which effectively lowers your strut back to the position it was in before you installed the coil spring spacers. Or you can pay top dollar for Old Man Emu or LROR 1.5" longer struts. I'm not sure how much difference it makes on this front end...travel is nothing to write home about either way in my opinion.

As for your gearing- I would suggest that your calculations are incorrect. Both my 2001 Vitara 2.0L 5 speed and 2003 XL7 5 speed are running the same diameter tires as what you wish to run, and they were both regeared (Vitara went from 4.62 to 5.13, XL7 went from 4.30 to 5.13) and drive 100% like the day the rolled off the showroom floor. The nice thing is you don't need to look to the aftermarket for these gears- any 5-speed Sidekick or Tracker will have the 5.13 gears in the diffs and they are a bolt-in install.