I've needed to update the thread, but I've been tied up at work - or running the boat.
First, the issue directly above (dropping ignition pulses) is sorted out and it runs great to redline.
I've got it mostly where I want it with the tune. I can crank it cold (well, as cold as the summer gets here) with no additional throttle, and it will warm up idling nicely at 700 rpm or so. Cold start video ->
https://youtu.be/SLRkwOEi32A
It holds that idle RPM with no issue now, dropping about 100 RPM when shifted into forward/reverse (only two 'gears' on a boat). I've also been able to lean out the idle some, helping with the smell when idling. It still likes around 13 AFR to idle, but with advanced timing there really isn't any smell. HUGE advance over the carb, where I needed 12.3 or so to idle well.
I've been able to lean it out in the midranges without seeing any signs of detonation. This is a major jump overt the carb, where boat angle cause fuel mixture problems (from changing fuel level in the bowls) - at 1800-2500 RPM on plane, I could never get the carb out of the high 11's AFR, now I run 13.3 or so. I spend a fair amount of time in that range, so I am enjoying the fuel savings.
After I got all that done, I turned Accel Enrichment on. This was a challenge, since there is not much needed at 2000 rpm up, but a lot needed at off throttle. Boats essentially act like a car with a loose torque convertor - put much throttle in off idle and the RPM jumps to 2400 in a second or less. At PSIG's suggestion, I solved this by increasing the VE in the cells just off idle. I also reduced the % AE some and increased the duration of the AE.
All in all, I am Please with how it has turned out. The Speeduino is an amazing system and fantastic community. Boat has never run better!
Current tune file is attached in case someone wants to reference it.