Your trailer is beautiful. I've got a Bantam as well and I'm having the same concerns as you (including wanting to convert it to an Overland Trailer while not destroying the originality).
I'm happy to hear that you're home and on the mend!
Concerning a few of your questions:
Tongue extension and backing concerns:
The longer a trailer is (between the hitch and axle) the easier it is to back ...it's that simple. Also, the shorter wheel base of the tow vehicle, the easier any given length trailer is to back. I have a Jeep YJ with a CJ front clip, a Scout 800V, a Scout II, my DD is a Single Cab Tacoma with a 6ft bed, and a '74 F250. I listed them in that order because that also gives you 'easiest to hardest' on any trailer for backing. Bantams are SHORT. They're pretty difficult to back (regardless of the tow vehicle). Start out trying to back your trailer in a straight line (take it to a large empty parking lot). If you can't see the trailer in your side mirrors, remedy that problem FIRST. Once you learn to back it straight (and it takes some practice) your life will get much easier. All that said, I'm extending the tongue on mine. I'm definitely keeping the A in place, but I'm still trying to decide whether to add an outer "A" and tie it in to the existing frame, or just putting a longer tongue on with strapping down the sides where the center cast section bolts on. Regardless of which way I go, there will be a receiver mounted so that I can switch between a ball hitch and a more 'offroad friendly' hitch (lunette or one of the universal setups) as well as having the option to lengthen as needed and remove everything past the receiver hitch (on the trailer side) for storage purposes.
Tire choice:
As long as your ground clearance isn't a problem, I wouldn't swap tires (or wheels) unless you just wanted to match your tow rig. What you've got right now is very capable.
Axle upgrade:
If you're not planning to upgrade the frame and suspension (which would be insane given where you're already at), I wouldn't touch this. Your bearings and spindles are wildly overkill and if you went to a heavier 'rated' axle, you'd probably actually be downgrading from the bearings you have and you'd be in a situation where your frame couldn't handle what your axles could (...and frankly you're already there). As someone else already said before, if you want to match the wheels on your Bronco, buy wheel adapters and move on. There's absolutely no reason to mess with what you've got.
Powdercoat:
I have a 'budget' powdercoating setup in my shop (meaning a Summit powder gun and an electric oven!). I've powdercoated a lot of the individual pieces for my trailer, but I'm limited by oven size. Assuming that your powdercoater is even somewhat competent, you're not going to chip it. I have powdercoated tons of things, some (mostly vises and tools) were done specifically to beat on them to see how it would perform. The stuff is amazing. Don't worry about drilling and bolting....
I'm adding a solid top to mine (designed to clamp into the stake pockets) as well as a frame (that lifts) to mount a RTT (I want canopy areas for cooking in the rain while retaining less wind resistance while towing). All of this is being designed to be 'bolt on'. I'll have a handful of extra holes in the trailer, but if I ever decided to put it back to 'stock Bantam', I can throw all the original bits back on and weld up some holes. I doubt that I would, but I want the option.
In the end, you have to decide what you want. You have a beautifully restored original trailer right now. If you're willing to start over, you could design and build a fantastic completely custom Overlanding Trailer, or you could take what you've got and build on it. I'm doing the latter, but I understand where you're coming from. It would have been cheaper and easier for me to have started with a pile of clean steel, but I couldn't pass up the chance to build a Bantam into what I want (and mine was in much worse shape than yours!). Mine had one badly bent top rail and the bed was rusted out (I'm calling it 'project tetanus'). It was destined for the scrap yard. The first attached pic is the 'before' picture. The second was after a couple of hours of straightening to the aforementioned top rail.
I'm about halfway through sandblasting and filler primer at the moment, but the axle is fully rebuilt, model A taillights are sandblasted, spacers (for flush alignment to the trailer) have been fabricated and the components will be powdercoated black as soon as I find time, and I'm still working on a final design for the cap and lift structure for the RTT.
Regardless of how you decide to move forward, you've done a lovely job thus far and you should be proud!
(and no more pics of mine will be forthcoming until it's at least fully primed)