Changing the Trigger Tooth to 1 ended up placing the timing marks right where I wanted them.
I was then able to time the engine with great difficulty, as the timing would change a lot after restarting VEMS, and took many tries before it stayed consistent. Now that I re-read your advice, I realize I've done that part backwards maybe. Anyway, I got a decent, reproducible 7 degrees BTDC dialed in (best I could get with my bass-ackwards method).
I then tried what you said about doubling the ignition output. That gave me two quick sparks, a pause, then two quick sparks. It seemed to be working, so I put the distributor back in the mix. I would get sparks for plugs 2 and 4 only. I then upped the ignition outputs to 4, which gave sparks on all 4 plugs in the correct firing order.
I put the plugs back in the car, set the fuel injectors settings, put the fuel pump fuse in, pulled the WB02 out of the exhaust and gave her a crank.
Success!
She started, and idled. I've spent about 2 hours fiddling around with things trying to get stuff to work, like the radiator fans, and the idle control valve.
Mainly I'm having issues with the idle control valve, but I'll take that topic back to my project page.
Either way, the car runs, and responds to what little tuning I've tried. This is a huge step, and I'm pretty happy I've managed to get this far. Apparently VEMS and I don't mix when it comes to ignition. Rob, do you have any idea why I have to have it set up the way I do? There's got to be something wrong, right?