Glamis4evr

Okay so a few years ago I inheritied a 1990 Kawasaki 650sx from my uncle. This was his spare ski and he was sick of dealing with it. He brought it out to the river for me and while I was riding it, the pisser stopped working and the ski started to overheat. When I took off the head, I realized that the O-rings had started to leak from the heat. This was causing water to get into one of the cylinders. I replaced the o-rings and the head gasket and went out again. The ski was running great until I woke up Sunday morning and noticed it sitting underwater on the beach. We took out the ski, drained the water, pulled the plugs and shot the water out of the motor. It then ran fine. I went again the next month, to find out that I had some electrical issues. Fixed those, but then noticed that it was running on one cylinder again. During the winter, my father and I completely took the ski apart. The motor was disassembled and had a chunk taken out of the top of one of the pistons. We honed the cylinders, replaced the pistons and were good to go. I rode the ski a whole weekend with no problems until it stared taking water on again because the water box became disconnected. I again drained all water, reconnected the waterbox and let the ski air out completely. It continued to work the rest of the weekend. As I went back two months later the ski was running great. When I was at full throttle, it felt as if the plugs were fouling because it would start to bog down. If I let off and slowly got back into the powerband, it would take off again. This was a little frustrating, however I just couldn't go full throttle. As I was about 2/3 throttle, it started to happen again. I started to let off, but it suddenly stopped. It would not crank again. Frustrated, I took a compression test. 25psi in one cylinder, 0 in the other. As I took it apart at home, I noticed the same chunk taken out of the exhaust side of the rear piston. Do you think it is running too hot? Or is it running too lean? I premix my gas at 40:1.