I will say one thing....
I went through a problem with my choptop when I replaced the motor with a junkyard one. I spent a couple weeks bashing my head against the wall trying to get it to start. I had good compression, I had strong spark, I had air and I had fuel. By rights it should have started like that, but no. I replaced the distributor, replaced the plug wires, coil, battery cables, spark plugs, plug wires, re-set the distributor several times, swapped the intake and fuel rails from my old 2.9, checked fuses, checked relays, checked fuseable links, replaced the TFI, and did a ton of other things.
I was totally frustrated and despite several experienced people trying to help me, it was still a no-go. So when I ran the battery down for the umpteenth time, instead of pulling it and sticking it on the charger and going for a beer or three, I pulled my Ranger next to it, left it idle, and hooked up the jumper cables. Let it sit a min and tried the BII. Lo an behold.... it fired right up. Never had another problem since.
Don't ask me to explain what happened. About all I can think of is maybe the extra shot of juice from a running motor with a good battery and alt was enough to do something. I'm not sure that hooking a stock BII up would do the same sort of thing though, my Ranger has a 130 amp alt (or somewhere thereabouts) and the stock BII alt is only something like 85 amps.