You flushed the block and cooling system with water; did you try any of the flush/cleaners? If it ran cool before, you may have buildups in the system that plain water will not remove.
Did it ever run cool with the new radiator? I wonder if the new radiator is correct for your application? Maybe too small, or has too small of passages. too little surface area?
Has the tranny cooler always ben mounted out front? At low speed/low rpm that could affect air flow.
Although the plugs are new, what do they look like after the engine has run, especially at low speeds/rpm. Check them for a lean condition.
You are running this closed loop on the FI. Where is your O2 sensor for the FI controller mounted? If it is not in the proper place on the header, it could lean out the mixture, especially since you are running open exhaust.
Someone else mentioned hoses; that's a good thing to check. I had that happen once on my old CJ5. the hose was old, and collapsed easily once the coolant was warm. My old V6 had a small heater hose section that blocked or pinched easily, and would cause problems...
The idea about the timing, well worth checking. It could cause it to run hot if it was off. It would also confuse the FI controller and compound the situation.
Most of your replies indicate a worsening condition before most of the mods.
I think, IMHO, I would put new hoses on just because. They're cheap, and good insurance when your miles in the back country. Check the timing; that's cheap and simple to do. Put a good cleaner/flush in the cooling system, or take it to a mechanic; sometimes they have better chemicals and stuff to clean/flush it better.
One thing I did not ask before... Do you have a big Warn 8274 winch in front of the grill blocking flow? A bug screen?