water in deisel engine... help?

i have a komatsu pc50mr mini excavator. It got flooded and water is in the oil/ Water got into the air filter and muffler. ENGINE was not NOT RUNNING during flood. did run prior to. SOme over heating and later some black smoke as the angle increased to about 40 degree downward pitch.

what am I to do.... put a charge on the battery but heard clicking and sparks from the charging battery.