HePe2008

HI I need some help. I own a 97 sea doo speedster, I was on a river when a alarm went off. eeeek. I wasnt to concerned at this point because sometimes this same noise has sounded when my key wasnt on all the way. So thinking not to much of it I opened my hatch, nothing seeming to wrong I closed up and continued down the river for about 2 to 3 minutes twisting the key hoping the noise would discontinue. Well it did not and I decided to open the hatch again. When I did, smoke pored out. I shut down both motors and waited for smoke to clear. When it did, I could see my driver side motor was very dark in color. Both the top of the head and the exaust manifold were changed color from getting so hot. I know I wasnt supossed to run the boat on one motor, but tried anyway to get back to shore because dark was closing in. When I tried to start the passenger side motor, it would fire up but not stay running. I ended up getting towed back. I let the boat sit for 2 or three days before trying to fire the motor to see if it has seized. It did not. I ran a compression check and both motors had good compression. My question is, Im wondering if I should tear down the top end to look for scoring and replace the seals. Or try and run it. Is there a possibility the motor is ok? I guess I should mention the reason for the overheating is a piece if large tow rope got wrapped around my drive shaft and stoped water from entering the jackets to cool it. Also the a oil line for the motor melted off which is why I bielive the other motor shut down seeing this line feeds both motors. I NEED SOME HELP... ANY ADVISE?????