So i just picked up a 94 FD this past weekend the car has a untuned PFC with a 3" TBE no cat. On cold starts it starts up and idles at 800-1k RPMS but the engine has a rough shake feels like a constant misfire. I'm going to check the compression but wanted to check to see what you guys figured the issue might be?

 

my guess is just what you stated.
Untuned PFC.

 

If compression is good...and if it starts easy it probably is, I'd change plugs and at least check wires both leading and trailing. Consider cleaning grounds which are listed in the Factory Service Manual (FSM) available in a free download in the 3rd Gen. Stickys. You can also add additional grounds too...engine to battery, battery to chassis, chassis to engine. Some decent fuel injection/fuel system cleaner wouldn't hurt either. I like the BG44k or Chevron Techron stuff and run it with about half tank.