Hiya,
I just did a quick skim of your thread, and it looks to have many similarities to a prob I just figured out and fixed on my 1990 Alpha 1, Gen 1 3.0. I had no-start condition. At first thought wasn't getting enough fuel, and would occasionally sound like it wanted to start, but would would only fire enough to make it sound like it was close.... occasionally a backfire. Discharged battery 2x thinking it was just badly flooded. Then decided it must be ignition related... Did diagnostics (mine has DDIS ignition system), and coil came up with bad R readings. OK, geared up to buy whole new ignition system and swap it out (since DDIS coil is obsolete part). BUT... continued on with next step of diagnostics, which is the shift interrupt switch... I disconnected it, (on mine is normally open, but transiently grounds coil when closed) and motor fired up with a mere bump of the starter, idled nicely, and rev'd in N... no prob... So I think OK, neutral interrupt switch is bad and was perpetually shorting ignition (probably accounting for whacked coil R readings).... But, then wanted to check how boat would shift without a shift interrupt switch and found that it shifted to FWD fine, but I had no Rev. (?) Then pulled the outdrive and discovered lower shift cable was toast as it had a big kink by the slide. Replaced it, reattached N cutout switch, (which now works fine) and boat runs great.
So I went from a no-start, must be ignition failure to the actuality, that it had a bad lower shift cable that was putting pressure on the linkage that engaged the shift interrupt switch. It seemed to not completely disable the ignition, but enough that engine won't start.
I realize that the shift interrupt switch operates differently for different years, but you might want to investigate that and try bypassing it (which could mean either disconnecting it, or jumping 12V around it depending on how it operates) to see whether it might be screwing up operation of an otherwise good ignition system. If so, then you'd need to investigate whether is a problem with the switch itself, or something else (like shift cable).
Just a thought.... good luck!