[patrickt]

That's a pretty fancy carb. But a Holley is still a Holley and cracking open your secondaries is just the old school way to do it when you don't have an integrated idle bypass valve, which you have. 98% of all Holley drivability problems are the primaries not being set properly on the transition slot, the idle mixtures being off, the floats being off and the change in under hood temperatures that makes the air thinner in a car like your Cobra.

But, we could be completely wrong and you really have a bad spark problem. Maybe the MSD box, the coil, the pickup, who knows. The absolutely correct way to approach your problem would be to swap a known-to-be-wonderful Holley 750 Vac Secondary from someone's car at the local Cobra club on to your car and see if all of sudden the problems were gone. Is that a possibility in your case? It doesn't even have to be a Cobra club, an old Ford or Mustang club would do just fine.