Help needed with my 2006 90HP Merc Optimax PLEASE

I have a 90HP Merc optimax that I used to love when I had it in florida and now since bringing it to Michigan it has been nothing but headaches starting to think it doesn't like the freshwater. SO heres the problem I've put over $3000 into the motor at a marina this summer and it still doesn't run right. I just recently took it to the shop because it wouldn't idle and had no power one day then run like a rapped ape the next, it would run at only 4500 rpms they had it for three days and ran the crap outta it on the water hooked up to the computer and it never missed a beat so they replaced my alarm that wasn't working and told me nothing else was wrong with it and billed me $300 bucks for it. I brought it home put it in the water and it started right up and idle smooth as can be ran great for a little while then I took on some water in rough seas and it started acting up again wouldn't idle and had no power. I fig. something was shorting out so got home and pulled my harness outta the hull and found a bare wire where a mouse had chewed it so I cut the harness off a foot from there and re-wired my ignition thinking I solved the problem but it didn't I'm still having the same problem. If I idle up the motor to get it to stay running I can unplug my #2 cylinder and it stays running so I am thinking it is only firing on two cylinders but don't know the cause. PLEASE HELP