Motorcycle Repair: S&S popping in rear cylinder, straight pipes, rear cylinder

Question
QUESTION: 88ci S&S, vance and hines straight pipes,super E carb 1 7/8,
thunderheart ign,  pops out rear cylinder after you let out of throttle,breaks up at 3 grand (sometimes),pops out of carb occasionally but not regular,have replaced intake flange seals( no difference),have checked plug wires, then found red coil wire rubbed bare, taped it (no difference),
what else should I check before I change Ignition? could it be worn valve guides?

ANSWER: Pull your plugs and let me know what color they are
Mike

---------- FOLLOW-UP ----------

QUESTION: new plugs run 20 mins,clean!old plugs were black as i had been experimenting with jets as of now .072 main and .0295
intermediate

Answer
Since your old plugs were black, then you are fouling your plugs. Fouling plugs are due to either a weak coil, weak plug wires, or wrong jetting.
I would start by testing the coil and plug wires to make sure they are ok. If they are good then I would check the jetting on the carb.
If you go to the S&S web site there are great instructions on jetting your carb.
Good luck and happy riding
Mike