Yeah, it would've been helpful to know the EXACT reason but since it seemed to work I wasn't re-fixing it. LOL

Even if you have a isolator you can't run batteries on both...it will still overvoltage the system causing ECM problems.

Assuming your feeling and seeing the diff in that one engine. Rpm loss coincides with boost gauge?

yes it is map sensor is good so is iac

Have you tried swapping the PCM with another engine?

GF?

yep no change

That is a Bad Idea running batteries on Both , seen that melt an Altenator on the Port Engine smoke the wiring harness . Then burned the whole back off the boat!
The transients that the combined Charging systems setup, when combined, will wreak havoc on the ECMs. New Belt , New Tensioner then Id swap the ECMs and Boost controllers between Engines and see if the problem follows it

did ecm swap new boost had it no the computer to check map sensor all good .

The PCM uses inputs from the MAP sensor, crank sensor (RPM) and the Throttle Position Sensor to calculate the signal it sends to the boost controller. Barring any mechanical issues with the engine you might want to try a new TPS. The TPS is a potentiometer and it might have a bad spot that is causing the output to fluctuate, which might explain why it works sometimes. BTW, the TPS is AC Delco part #213-911

GF?

did compesstion check on all cylinders there fine tps cheap enough will try . would that throw a code . I got a race vision smartcraft display nothing