2004 Speedster 200 P0352 #2 coil fault

[IDoSeaDoo]

Took the speedster out on Saturday and immediately noticed a Check Engine light on on the startboard engine. It also ran like it was on 2 cylinders. Turns out, it was. Got the P0352 code: ignition coil #2 short circuit- open to ground or 12v. Swapped with #3 coil, problem persisted. Put #2 coil on #3 plug and verified a nice beautiful spark, so it's not the coils. I checked the fuses and disconnected and reconnected the plugs from the ECU and MPEM with no luck. Next I'll be checking the continuity, hoping for a defective wire harness or something. I REALLY hope it's not the damn Engine Management System computer, but that's what it's looking like at this moment. I've seen several other forum posts on the same issue, and the only one who actually wrote a conclusion claims it was the computer. This seemed to happen right after I installed a new battery, so maybe I hit something with it, hopefully, it's just a damaged wire or something easy

Anyone have this issue before?

 

[IDoSeaDoo]

Which part is the one tied to the key? I have two engines, and each has this Siemens EMS module. However, the boat only has one key. There is a thing that looks like the ECM that houses the fuses, but I'm not sure if there is one for both engines. It has fuses for cylinders 1-3 ignition, so I'm guessing those are engine specific. I believe my problem is the EMS, so I'm guessing I will not need to reprogram my key, right?
Also, I'm guessing I can use any EMS module from any 155hp boat or ski, right?

 

[IDoSeaDoo]

Anyone know if I can use a Ski ECU in a twin engine boat? I'm not sure what module the Key is tied to.