Have you verified that the lower shift cable and the shift cutout are in good shape? If the roller/follower gets a little out of the V groove it will cut power to the ignition. I'd suggest that you physically watch the shift cutout underway. Also along that line, does the lower shift cable come out of the transom plate and make a big easy curve behind the steering ram before it ends up at the shift plate? You can't have kinks.
I wonder if you were to wiggle the harness wiring between the distributor, coil and the Thunderbolt HEI, if that would cause a miss...I'd maybe do that with a stick in case of stray voltage.
It wouldn't hurt to poke around in the gunwale where the wiring runs to see if you can cause the miss there.
What about the master plug? On my 88 I ended up rolling little bits of emery cloth and also using teeny wire brushes for the sockets and male plugs. I also opened up the plug ends a little with a razor blade. They are split down the middle and opening them a bit improved the contact inside their sockets.
