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Bad ECM - 05 vlx w/ 340 monsoon

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I've got a quick question about the ECM on an 05 vlx w/ 340 monsoon  if anyone here has the same boat. For the 4 years I've owned the boat I've never had any type of check engine light or error code but I've overheated twice and now have a misfire I'm dealing with that the knock sensor isn't picking up. I've built the code reader to check also but it only displays the 12 code saying everything is normal. Does this sound right? I've read a lot about limp mode, even on older boats and I'm surprised it doesn't work on mine. There's also no buzzer either but I think the previous owner probably ripped it out. 

I'm asking because my dealer is telling me I need a new ecm because it's not reading codes, but I know it has worked before the current misfire issue i'm having so I'm pretty sure it's a not an issue with the ECM.

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Ive got a 03 vlx  with a monsoon.  I’m not sure of the differences between 03 and o5 , but as far as the overheat have you checked the hose at the bottom of the oil cooler?  Theres a grate in there that catches particles of the raw water impeller and such over the years.  My  03 only had one owner before me and he only had it two years.  I never had an impeller that appeared damaged over the years,but when I finally checked that a few years ago chasing an overheat cause and it was almost blocked with little pieces of rubber. Could have been in there for years for all I know.  

 What are the symptoms of what your boat is doing besides the misfire? I ask bc I have recently run through about everything chasing down a problem of my own with low rpm and sluggish.. I finally pulled the injectors and they were in terrible shape.  

I’m assuming your dealer ruled out basic iginition things?

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Long story about the over heat but 3 years ago my temp gauge in the dash went out.  Next time I was out, I told my buddy to shut off the valves for the ballast since the tanks will fill up on their own and we were in salt water. He shut off the water intake instead and we ran the motor until it basically seized, not knowing it had overheated because the gauge didn't work and the boat doesn't seem to have any other warning like previous years have. Part of my question is why do the 05's have nothing when previous years have oil pressure switches and temp switched that will beep when they go beyond the limit.. Anyways I was able to rebuild the motor over the winter and was back on the water next year, mostly from the help on this forum.. so thanks to everybody here! 

I'm not positive but I feel like the misfire has been going on for all of last year but slowly progressing and getting worse. I was hearing random popping out of the exhaust at higher speeds and now I can hear/feel it constantly at idle and it's much worse under load. I've done all the basics and had the injectors cleaned. I think I only had 3 injectors that were actually functioning correctly but they all came back working good and it didn't have any effect on the problem. After putting them back I think it might have even made it worse. I'm suspecting that it's ignition related now, either icm or coil but I ran out of time to work on it last month and decided to take it to the dealer. I was hoping the dealer would check for ignition/fuel related things, but the only thing they've told me after 5 weeks of being there is that they think the ECM is bad because it's not showing any error codes from the misfire when they hook it up to a computer. Which leaves me wondering if the ecm is actually bad because I know it has functioned perfectly fine without throwing any check engine warnings or beeps. 

Compression test is good. I've changed plugs, wires, cap and rotor, fuel filter, fresh gas, and cleaned the injectors. Timing is also good and I've test fuel pressure at idle and it checked out but I wasn't able to test it under load. 



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