I assume you made all those changes to your car at once? If so, you just learned why you should only do one thing at a time and verify everything is in working order before you proceed to the next upgrade. It lends to targeted troubleshooting when things like this happen.
IMO, the inline six can be a little more difficult to tune, with our long log intake that contributes to mixture variances between the center cylinders and the outer cylinders (well, all of them really). So while Xargon is correct by observation, FSD is right in an absolute sense - there is no reason your car can't be made to idle smoothly. You'll just have to put some work into it and we'll try to help.
from my side of the cracker barrel, I'd try unhooking your AC, I don't think that's it, but it simplifies testing and it's October (though I don't know where you're at).
you undoubtedly have a timing light, does your timing vary at idle? If it doesn't (and it shouldn't), and you have good power while driving, it shouldn't be your vacuum canister. The can on my load-o-matic is shot, symptoms are fluttering timing and zero timing change through the rpm range. All that means no power and virtually no drivability.
I also have a miss, if I detach the wires from the plugs, 1-5 bogs the engine, 6 has no change. #2 shocked the heck out of me, so wear heavy gloves or something. A miss can be a bad cap, a bad plug wire, a bad plug gap, incorrect plug wire mapping, or a lean charge from your carb (I think, I only play a mechanic when no one is watching). For the rest of the forum, that tapping, isn't that a late fire popping out the exhaust valve, or an unburned charge lighting off the hit exhaust of another cylinder? It's a little hard to tell. Might need to back off the timing a little. You also might want to get an O2 sensor to see what's coming out of your pipes.
I doubt it's your pertronix install, though if your plug wires are old, messing with them during the upgrade might have damaged one or more.
