Welp, it was indeed the box. I extended & connected the stock ignition coil wiring from the fender, and it cranked and ran long enough for me to set timing.... maybe a full minute, which it has not done since the car left me stranded. So, I'm pretty sure it's good to go, now. I'll probably button it up on the first available day after xmas... Monday, maybe...
So, what do you boys do for timing retard and a spark limiter on nitrous systems? Is there any other option than a tuner/stand-alone? I think I'll end up putting another box back in the car for those capabilities, but it's not going to be a 6AL.