Excessive shaking during rev up

I just installed a new stock type distributor on my stock 289 65 Mustang. It came with the old style points and condenser. I had been using the Petronius igniter in my old distributor but I decided to give the points a try since they were new anyway. Well to make a long story short when I installed the new points and condenser in the new distributor the motor fired right up and ran smoothly. But the engine shakes tremendously on acceleration and when I installed the Pertronics set up it did not run as smoothly but the engine did not shake on acceleration . Has anyone ever seen the Pertronics igniter go bad? It has a stock coil I do believe. I recently put in a new Timing chain and made certain that the dots on the sprockets lined up at 12 and 6 o’clock. I have also adjusted the valves several times. Any help with this problem would be appreciated.
 
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Well after the usual idiot checks (firing order, decent spark plug wires, fuel filter, fuel pressure, etc)
Pertronics can be picky about its grounding Check all the way back thru engine grounds and battery grounds.
Coil could be gong bad also.
Good luck.