I experienced the identical problem when first starting up our 1966 Mustang last summer. I could get the MSD system to spark manually when doing as FatBoy described. Once I did it with my hand in the coil discharge path and DAMN that hurt, but the engine would not fire during the starter cranking cycle. I tried a fully-charged battery from my F350 diesel Powerstroke, and it made no difference because the battery was not the root problem.
After a week of part time diagnosing, some calls to MSD and a lot of back and forth checking, the problem was:
I had chosen a 12v "key on" wire to the 6AL box
that wasn't providing the 11v minimum during the cranking cycle. When I chose another wire to be the 12v "key on" wire, the engine fired up immediately.
David