Is this an SC? The first time I worked on an SC...I forgot that the distributor was turning counterclock rotation. I ended up with a very unhappy engine, backfiring missing and very poor performance. With the trottle opened up, higher revs, the car seemed to run a little better.
I agree that a troubleshooting system of one thing at a time makes really good sense, especially taking notes while doing it so you can remember where you were if interupted.
sounds like a crossed wire, or maybe a loose distributor cap.
Good luck!