OK, so it sparks at the coil when the lead from the points is tapped to ground, but not when cranking…So, it does seem like you will have to remove the flywheel, unless the ground lead coming from the ignition point plate is not making a good connection. Perhaps the leads are frayed/broken.
The points are probably just a little dirty, there are two sets which are gapped at .010". The anti reverse spring could be causing a problem if it is somehow stuck grounding out the circuit, doesn’t seem likely though. The anti reverse spring is probably in OK condition and does not need to be replaced, but it is a needed item and should be replaced if it is NG. I am assuming you have a decent OMC manual for this engine that will explain servicing procedures in great detail.
Yes, if those battery cables were crossed, even for a second or two, I am quite certain the alternator rectifier diodes are shot, the shift circuit diodes may have been damaged also. We will get back to this after the ignition is straightened out. Be sure to check the resistance of the alternator windings while the flywheel is off, it is unlikely that crossed cables damaged the windings though.
Great news, the gearcase shifts OK, I thought it would. Did you fill with OMC premium blend? Normally, I would recommend doing a water pump job, but not in this case. Again, I don’t want you digging into this thing any farther than absolutely necessary. Once the ignition is straightened out, you can search for a decent control box/wiring harness…

Don’t know just how you tested that rectifier, but there are six diodes that are checked with an ohm meter set to the high scale. There are a few diodes in those shift diodes as well, the manual spells out the test procedures. The alternator winding resistance value you mention seems about right, will attempt to find a manual to confirm.
That "clipper circuit" is a lame attempt of protecting the powerpack/amplifier from voltage spikes resulting from poor battery connections. The alternator windings are shorted/perhaps grounded when high voltage is sensed. The procedures for testing it are in the book, although a little vague/confusing. Like I said, the rectifier is usually damaged quickly, even if the cables are reversed only momentarily. I suppose there is the chance that the cables were never reversed in spite of the red tape on the negative cable.
I would agree, the flywheel was probably not torqued properly if it came off relatively easily, be sure the tapers are clean and dry when you reassemble. The coil threads into the distributor, its voltage is routed to the rotor through a tab in the center of the distributor, the outer tab on the rotor delivers voltage to the four plug wires through copper/brass tabs on the outer edge inside the distributor. There is the possibility that the distributor/rotor is leaking/arcing causing the no spark condition, this can only be checked using coil tester to supply power to the distributor, then probing for leaks. These items are pretty expensive if you can find them, so I would no just replace them unless you can confirm they are leaking/arcing.
Did you have a look at the points? Are they gapped correctly? Was the anti reverse spring present, was it working correctly? If the ARS is somehow jammed/stuck on the ground tab, this would cause a no spark situation. Be sure to use a little Loctite on the stator screws during reassembly.

I agree, the forward gear fail safe always seemed like a good safety feature to me also. OMC claimed the coast guard didn’t like the system, maybe if was actually the OMC bean counters who didn’t like it…