So I thought everything was good until last night when I drove the car to the store. About half way there it started to run a little rough again. This morning I took it for a drive and it was good for about 3 minutes and then started running rough again. I think that maybe one or two plugs might be bad and once they get some heat in them they start missing. I have a set of Autolite racing plugs that I ordered from Summit that I'm going to install tomorrow or Saturday and see if that is the issue. If it isn't then I'm at a lost.

Sounds like the PIP

What's the PIP?

Basically the sensor inside the distributor. Could also be the TFI module on the fender.

I have an MSD distributor so if you're talking about the magnetic pickup module inside it that has already been replaced not that long ago. I had an issue at one time where the car would cut out above 5000 rpms and I thought it was the pickup so I ordered a new one from Summit. One of the wires on the old one had worn through and I figured that was the issue. I still had the issue after replacing but it turned out to be because of the hole in the rubber elbow on the intake tube. Once I replaced it the car ran great.

I'll replace the plugs since I already have a new set and see if that resolves the issue. If it doesn't, what's the TFI module? Is it on the passenger side?

Yeah, under where the stock intake was. A PIP module is in ever distributor, stock or otherwise. You need to remove the upper bowl of the distributor to get under the piece that the rotor set in.

I had Phil test drive the Cobra tonight to see whether he thought what I was feeling was a missfire or a vibration and he says it's a vibration. My next step is to check the harmonic balancer to make sure the new one is 28oz and not 50oz. If it is then I guess from there the next step will be to check the flywheel. If both turn out to be correct then I guess the engine comes back out to have it rebalanced.

If you had the wrong weight on there that thing would shake the vehicle apart. It would be nearly undriveable.

It's not a horrible vibration. It just feels like a misfire but you feel it more under decel which I was too frustrated to notice before Phil drove it.

Thats not the balancer then, I would still check, but if it was you'd definitely know.

I'd check the pressure plate, motor mount, trans mount or possibly the pullies.