Typically these bikes will go all the way over your ankles in water without an issue and almost to your knees. If your foot pegs were barely in the water it wasn't deep enough to get water in the engine through the intake or exhaust and the engine would barely even be touching the water. They will die easy in a water crossing if you don't lay on the gas due to extra resistance from the water pressure. As to the damage in your engine, I think that was done long ago. I have over 46,000 miles on mine now. I have ridden through water over my ankles on multiple occasions and at 42,000 miles my engine was spotless compared to that. Sorry to hear about the bad news. There is no telling what that engine has been through so it may be best to replace it to get you up and going and then tinker and rebuild at a later date.