Check your ignition and timing first. The coil is always suspect in this type of circumstance (relatively cheap and easy, too). Ignition boxes can exhibit this type of behavior when failed (or failing). I have seen all these culprits cause this kind of problem.
I'm actually having this kind of problem right now too. I have a new timing chain on, new spark plugs, new wires, msd coil and new distributor cap and rotor. What else do you think it could be... O2 sensors maybe?