I'd start at the battery, starter and ground lead connections. Then the ten pin connection.
Guessing corrosion somewhere that was made better/worse with the motor r and r
Patina on the flywheel looks like a semi sinker at one point
Saved most of the running gear, ditched the transom assy and trim pump but kept y pipe, inner plate, p/s pump and actuator (old school greasable)
But....
People helping on this forum didn't "come up with the problem", your engine did and you posted?
Is it okay that I'm confused reading this thread?
Disconnecting the battery while the engine is running will surely damage the alternator. Time to replace
When was the serp belt last inspected/replaced?
Can't test a marine alternator is code for "we can't even test any alternator". Very few auto parts stores had a setup to bench test...