engine missing

About 3 days ago, I got my 327 engine running in my 86 chevy pickup. From the start the engine was skipping and backfiring a little when i gave it the gas. Just enough to notice when you were going down the road. We set the timing and put new plugs and wires in. The same day we got it running, the gasket between the spacer and the intake manifold blew out. It blew out because i was using a holley gasket rather then the correct one for the manifold, a quadrajet. We were in a hurry and didnt have a quadrajet gasket, so my friend sealed the spacer to the intake manifold with some "Indian Head, Gasket Shellac Compound". After that, the truck still missed when under the gas. Today when i woke up, i decided to get a new cap and rotor. I drove my truck to my friends house and it ran perfect. No missing or sputtering. We proceeded to put a new cap and rotor on, and it ran fine. I drove all over town with open headers and it was fine. I then went home, and later went to my friends. When i was a my friends i let the truck cool down, and then later i gave him a ride in it. The truck started to skip and miss like the day before. What is the problem, some times it does it and some times it does not.

Sounds like a plug wire to me. Look closely at the spark plug boots.