2000 Kawasaki 1100 STX D.I. ecu problem

I put my jet ski in the water at the beginning of the summer and the battery was dead. Since I fully charged it beforehand, I put a new battery in it as the old one was four years old.

The jet ski fired right up, but the battery light was flashing. My kids ran it for 3 to 4 hours before it went into limp mode and then would not restart. I charged the new battery and it ran fine again, but now the battery light was flashing and the engine warning light was now on. We put a voltage meter on it after running it awhile and it was low. Apparently the machine was not charging the battery. Guys around the lake thought it could be the stator or ECU, but could not guess which one and said to take it to the dealer.

I took it to the dealer and they said the regulator was shot. Since it was within the ECU, it would cost me $1300 to replace the ECU. I brought it home to explore my options before I cough up that kind of cash.

Any advice on this problem would be greatly appreciated. If it is the ECU unit, does anyone know where I can get it rebuilt or buy a used one ?

Thanks