My theory is you have an air leak somewhere, a leak down test before dismantling the engine would have been the thing to do. The air leak is mainly/only affecting the left cylinder causing it to run lean. The left cylinder is uber lean, forget about the carbon deposits. Your jetting is probably rich but that would not cause serious problems, just make the bike run a little crappy, you would notice at WOT, but your overall system for that cylinder esp. is lean lean lean.
You either boiled off all your coolant just from the extra heat, or the coolant leaked slowly into the cylinder got boiled off there and then once it was low/gone your coolant leak turned into an air leak into that cylinder compounding the problem. Since the air leak is affecting the left cylinder the right piston doesn't look as bad, the marks on it are most likely just from collateral damage so to speak due to the excess heat of the engine.
If your cylinders are in bad shape or even questionable shape, I would probably just look to pick up a whole used engine off ebay for a reasonable price and be done with it. New engine parts or even just used parts themselves, and engine work are not cheap but whole used engines can be found for decent prices.
Not overly familiar with the jetting on the pre gens or what your setup is like but just for comparison, my new gen has pods, race exhaust, and advanced ignition timing and I run a 108 keihin main jet at about 2000' elevation and in temps down to 20 degrees F. Been running it this way for several thousand miles not even a hiccup.
108 keihin is somewhat comparable to a 104 dj
P.S. when you post pictures of the pistons make sure you take pictures of underside as well and post them
