NICE! Those are my favorite rims! I'm looking for a set for my '87.
The banging problem is probably not your transmission, but your transfer-case. The BW1339 full-time transfer-case used a chain to direct *all* power to the driveshafts, both front and rear (not just the front like newer cases). When that chain stretches, it can jump the teeth of the gears, causing that noise you hear. The solution is replacing the chain; BJ's has them:
https://www.bjsoffroad.com/QuadraTrac-C ... _1598.html
I thought Power Steering was standard on the J-20; no matter, you can add a pump with the brackets from any AMC V-8, get a rebuilt J-20 steering box (they had bigger components than the J-10 or Wagoneer boxes), and just add the appropriate hoses (make sure to match the fitting style, flare or o-ring, on your pump and box)
I don't have any solution for removing the rust; I wire-wheeled mine down and coated it with POR-15, but that wouldn't look factory for yours.
Windshield leak is likely from rust; solution is to cut out the old metal, form new pieces, then weld it in. Anything else is just a bandaid that won't last.
There are no replacement over-the-counter tailpipes available, so custom-exhaust is your only option.