1978 Ford Grumann E350 5.8 running rough.

I've been working on the electrical system on my 1978 Ford E350. It was having problems shutting off after it warmed up. After replacing all the ignition components it ended up being the distributors pick up coil was bad. Problem is when we replaced the plugs along the way trying to fix it, it started running rough and acting like it was fighting a little to pull itself down the road. I did not change the spark plug wires from the distributor to the plugs. Some of the boots are getting a little warmer than the others. Any ideas what might be wrong?