Well I wish I could say it's a happy ending, but it isn't.
I ended up testing the distributor, the coil, and the switchbox and they all worked fine. After this and some further testing, I found that the spark plugs only seemed to work when the ignition switch hit a certain position somewhere between the run and crank positions. So I took apart the MerControl box and found that the wires at the ignition switch terminals and the ignition switch terminals themselves were in bad shape, so I replaced that section of wires (not the entire harness) and the ignition switch. Now the system won't even spark on some cylinders.
I guess I'm at a loss here. My only guesses at this point are that it could be the rest of the wiring harness, the battery, the plugs themselves, or maybe possibilty the trigger still, even though I thought I ruled that out already.
Sadly, this is it for now, I can't work on it anymore until next spring because it's too cold and there's snow here now, so I have to winterize the motor within the next couple days. Any last suggestions would be much appreciated. Thanks for everybody's help. I may continue this thread come springtime.