Your alternator should have one plug which connects both the sense lead and the excite lead. If so pull it and see if the issue goes away

first and foremost I would rule in or out the ECM if you have twins or another 555 engine to do a swap over -- and the smart way to test that is TAKE THE POSSIBLE BAD ECM / bad engine conditions and put that ECM on a known good engine to run. Do not do it the other way around because ONE DOES NOT WANT TO DAMAGE a known good ecm from a bad engine possibility. . A little fyi --The ECM turns on the main power rely. So what is the voltage when its gets hot ?

So I was at a Merc dealer and was talking to the parts counter and mentioned the problem. He said it was my plug wires. He said the computer measures the the resistance of the wires. I put a set of OEM wires on and BAM no more issues with the computer

Wow
Wouldn't have expected that...

EMI Interference to the max. YIkes.

What wires did you put on that caused these issues?

The 555 ecm does not measure any of that. It was rfi noise and my guess would be you had stray sparking off where ever caused the exact issues. Bad wires, not connected properly or however causing stray spark will act just like turn the ignition key off when the engine is running and then turned back on quickly plus that also causes the beep (s). Were these online bought plug wires. Possible sierra plug wires ? Also possible wires too close to the knock sensor and or wires too close to sensor depending how they were routed. Spark plug wires have nothing to do with no connection / communication to diacom scan from the dlc connector . nor will spark plug wires make communication come and go . Voltage large spikes and or power on off will cause scanning to lose communication, spark arching will cause this exact issue .

I agree with bup, had to be RFI interferance. seen it a few times with different things, some alt will screw a ECM up as well as MSD boxes

These were Taylor spark plug wires. Im glad you guys explained it because what i was told just didn't make sense to me.

Here is a video of it fixed.

idling is one thing and really not under load being stationary so with that said did you run it for around 30 mins thru out all rpm ranges including WOT for water testing ?? And with a scan tool hooked up ?

ECM 555 is NOT coil near plug nor is ECM 555 sequential fire like PCM 555 --- and like I said the ECM itself does not measure any outputs for ignition events. The 555;s are not that sophisticated compared to the current stand alone ECM;s on the market.

Yup ran it for a few hours under load. Ran very good and no issues at all. Had it all the way to 6k rpm