I do think the pertronix is compatible with the msd and I don't think that has anything to do with your problem. You ran it long enough to break in the cam. I run a similar setup and I had a consistent miss until I grounded the negative side of the coil to each head. As has been said the next step is a leakdown test or if you don't have a leak down tester rigging something up to push air into the cylinders to see where you get a leak. If you don't have a leak down tester you can take the needle out of a compression tester fitting and just hit it with air and see where air leaks on each cylinder. If you have sticking valves you should be able to hear it.
It sucks to get old but at least the expectations are lower. 65 mustang coupe, 306, 10.4 compression, 180cc homeported Chinese heads, funnel web, t5z, 4.56 gears in a 9 inch locker