1999 40hp 3cyl erstic spark. Need help

[KyBullet]

Had a guy bring me a boat that he has hooked the battery up backwards, and left it that way for 10-15 min. Off the bat I re wired from the switch about 2 foot up the harness. Went ahead and changed voltage regulator, still had erstic spark. He wanted to cover all bases so he got a stator and trigger. Boat is still doing the same thing. Try to time it and it's like it's not firing right because sometimes top dead takes a bit for light to flash. Any ideas?

 

[faztbullet]

Change all 3 CDM modules

 

[KyBullet]

Figured out if unhook the black/yellow connector from harness it runs just fine, key will still turn it off and then kills with will also.