Sounds like you have the exact thing we had. Here is the video of it. Ended up being a bad and shorted IAC. Got lucky and it didn't completely melt the harness.

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Personally, I would swap the Crank Sensor to a new one for good measure. I believe everything Bup/John says. I also believe that the Tach Signal is directly tied to the crankshaft position sensor. I had intermittent issues with my 496HOs, and NO codes were thrown. One motor was always lagging the other my 100-400 RPMs, and I was not in Guardian mode. (I owned a Rinda scanner when I had the boat.)

It ended up being a bad Crankshaft Position Sensor. As soon as I swapped to a new one, problems were gone. The boat was not dying out, but it was exhibiting some of the same other symptoms.
It will not hurt you to swap the CPS. The only thing is they are really stuck in there. Do NOT break it off when removing.

496HO: would IAC cause this? 1 engine lagging intermittently lagging 100-400 RPM

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Thanks I will ---- I am wrapped up for the next 3 days solid.

YES THE tach signal is from the crankshaft position sensor but the PCM has to see it and outputs that as well. Thats why it can be a pcm issue as well - that signal internally can become intermittent internally - Voltage issues is what knocks that out. Also the IAC can knock out that circuit internally of the PCM / ECM that is a very common issue.

Hey guys,

so after looking at all possibilities from what I am reading .. I changed the IAC valve , which needed changing as old one was definitely no good. So now no more 2 beeps per 2 min and motor runs well up to about 3000 rpm. For ****s and giggles I also put in a new CPS. I try to push the boat a lil and it starts doing the rpm drop with steady beep. What I do not understand BUP is if this is an internal issue in the PCM then why did this motor do same with PCM's swapped? Anyway.... very frustrating to say the least. For some more info the port motor also does lag in top end power and the starboard motor has to be pulled back to compensate.

Thanks again guys.

I know your reaching out to BUP and I am sure he will reply but,
personally I would not do any more to the boat,you need to take it to a shop where they are trained ,you need someone to scan for codes,review and understand what the data means,inputs and outputs from the ECU,sometimes a simple tap test will point out a bad ECU,you need someone with experience,
I know some have already diagnosed the issues as a bad ECU,
I would NOT touch the ECUs at this time,diagnosis might lead you to a bad ECU but I think its too early for that,let a good Merc Tech diagnose your issue first or else its a 50/50 shot at anything you try,
I hear a lot of people on here give advice,and a lot say go out and buy a scanner,I say this,I can go out and buy a stethoscope and hold it on my chest and I would have no idea what the sound coming out of mean,only a Dr can,I think its time you let a Dr look at your issue before you go any further,
my opinion,good luck and lets us know how it all turns out.

Thank you for your input on this... but I must let you know we did take this boat to a pro. I needed the intake (s) hoses done and did not want to spend the time or the sweat to do myself. I also had a mobil tech come by and go out for a ride.... this issue does not show up on any software. My hope here was to find someone who may have had this happen... and the video posted above is exactly what we are experiencing (interestingly they are on the exact same boat only 2 years older). I can't help but to think that when the shop was laying across the engines in order to get to those intake hoses they pinched or pulled something. I know, without a doubt I need a guy like BUP to go thru these ECU's But I still believe this problem is a hard wire issue and this boat will not run to full potential until I find it.

Anyway, I do appreciate any and all insight.

So, this is exactly what we are dealing with... and its amazing that the boats are almost identical. We did have a bad IAC on this motor. I replaced it and the code cleared and she seemed to run better but this issue is still happening. Was your problem a short in that harness? Last thing I want to have to do is start pulling wiring apart.

Anyway... check out video below:

https://youtu.be/IajRAGnBdxE

If I recall this went on for a while as to what your problem was - Or am I off base on the timeframe. Anyways a scan tool tool would have picked this up on the spot with the scan parameters showing an IAC out of spec even without a warning fault and or a displayed fault code. Wanted to make it known that just because a fault is not shown does not mean too much. Its all about the parameters to find issues to help pin point