@Wish - this thread may help:
http://www.correctcraftfan.com/forum/forum_posts.asp?TID=27323&title=gt40-intermittent-rough-running
Long story short --
solved!!!
This would be a very tough issue to identify unless you're super with electrical diagrams and know what you're doing.
Short answer: corrosion in the fuel injector harness caused the injectors to OHM out, making them shut down. Injector harness was testing at 30 OHM, should be no more than 12 OHM.
Mechanic cleaned harness and replaced corroded connectors inside the harness. Boat works great!
Of course, this took a long time to track down, mechanic swapped the ECM, distributor assembly, cleaned injectors, etc, etc so after 3+ days of labor charges, it's finally fixed, just a huge punch in the wallet. Glad to have it back, and hope this will help anyone in future.