It's been a little while, but I just wanted to give some updates incase someone else has similar issues. I had the suspect ecm reprogramed, but it didn't help at all. Same problems, same symptoms. Finally tested the reporgrammed ecm at a local go-fast marine shop, and got some answers. He explained that it looks like the controller has a bad driver in the computer that can not be repaired for a reasonable price. The ecm thinks it's working correctly (which makes it almost impossible to diagnose), but is incorrectly changing some of the sensor values.
Unless you can find a good used mefi 3, (ebay, etc.) then I need to replace it with Mefi 4b. Looks like the exact same controller, but the pins are in different order. So, either new wiring harness ($600) or change the wiring on the connections. This shop recommended a few suppliers that they work with. I ordered the new mefi 4b controller and new connectors for $748.00 I will be hooking it up sometime next week, I check back with results. $750 sucks, but it's better than the $2400 that FW wanted.
At the go fast shop, I saw some incredible rigs. 1100 hp 555s, double superchargers, 135 mph fountains, really cool stuff! We were laughing about dropping new power in our boat. For only $100K he thinks our 328v could hit 80! Tempting
