MSD problems

You should be able to rip out every single wire in the entire car and as long as you have cranking and power to the ignition components it will still run.
You missed something, or didn't tell us something.

Did you take into account that the MSD distributor might be at a different location as far as the rotor is concerned than the old one?
And change the plug wires in the cap to match?
Or move the drive gear to where it needed to be, so they match?

Any of this sound familiar?
Does the intermittent spark on number one happen about every 7th cylinder? :D
Sorry about the smart as in that last question, as I couldn't help myself.