HA! Well actually I have this boat down in SW Florida and it's quite beautiful here today. I am pretty much ready to do anything just two have the next 2 - 3 days on water b4 I go back to the big freeze. So just to be sure we are on same page... the last run I made I kept my trim in tighter than usual and did not experience the shut off. So, could it be just that over trimming could cause that intermittent pause? Also, the 2 beeps per 2 min... on my 496 mag HO (2005) back home I had same issue... changed IAC and muffler and have to tell you she never ran stronger or faster!!! Still very interested in having compsuters looked at so let me know next step... and do you need to know port or starboard as far as pcms go? Let me know thoughts.

thanks again!

If you find it easier to just have a real conversation over phone I dont mind sending you my cell #. LMK

sounds to me this guy you are speaking of should not be working on electrical issues,anybody that has a no start condition and does not check out all the inputs to the ECU before plugging a new one in has no business working electrical,yes a shorted out circuit will instantly kill a ECU,
but this is not what the OP is complaining about,he has a intermittent issue and the ECU notices that and does not like what it sees so it shuts itself down ,could it end up been a bad ECU,absolutely,I have repaired many because of bad circuit boards/solder joints expanding as the ECU get hot from engine heat and so on
I did not go and read the whole thread so forgive me if iam wrong,but did the OP state that he switched ECUs and the issue remained on the same engine?

With the PCM's swapped the issue remained on the same motor. However, upon further investigation we have realized that the trim adjustments were no longer synced to the gauges therefore Port Drive was over-trimmed. When we adjusted this problem manually we no longer got the shut off does that make sense?

Again, I do understand for sure that there are issues with these computers. The same computer that is having the fuel pump run on issue is the one that is throwing the two beep per minute warning. As I stated before I have a feeling my port motor needs an IAC valve but also both computers need some TLC

do you have dual water pick up on your out drives? I am assuming you have Bravos?
this is just a quess,but if you over trim you could be sucking in air along with the water and the water pressure sensor reading could get low and that could give you the 2 beeps you hear,

but like BUD said, all is a guess with out proper diagnosis

Yes... bravo 1's side and cone picups

the tach going to zero and the engine quick shut off then back on can happen when ever - Maybe you did not run long enough. Have no idea - its a very issue that can come and go when ever and at times good for days on end.

The trim limits are set buy using the scan tool if they are digital with smart craft or u might have mechanical trim limits. I do not know what your set is - not looking at what you have.

My post about ecm / pcm getting knock out was a jist for all info whom own these marine efi engines. As pointed out in the service bulletin with Merc outboard that I posted above - bad ingition coils can do the same and buy swapping over pcms - guess what --- you can ruin that known good ecm as well just by cranking over the engine ONLY. That is not uncommon to take place. I am saying this as added info for whomever including the outboard guys.

IMO you need someone that really knows how to work on these and has the proper tools and proper scan tools. Like I said you have more than one issue. And I would bet one PCM has a bad circuit internally.

And if your fuel pump stays on as YOU REPORTED can be another issue with that PCM. Too much dart throwing here and wasted time as it seems your issues are all over the place.

Ok.. thanks again. We are down here til Tuesday then back up to Long island. Not sure where you are located BUF but I can ship the PCM's to you if necc. Let me know what you need to get started.

thanks