CEL po304 after smog

I recently had my 03 Astro van smogged, the shop required me to remove the engine cover or I'd be charged $50 for them to do it.
I had this same procedure 2 years ago and had no problems reinstalling the cover.
Van passed smog no problem but I had a lot of trouble getting the cover to line up so I could bolt it on.
I finally gave up and was going to drive home and finish it there, but now the van wouldn't start.
It would turn over but it seemed like it wasn't getting any spark.
Well the guy from the shop helped me, we pulled the cover back off, jiggled some wires and it eventually started but ran really rough, no CELs though.
I drove it home and took my other car on some errands, when I got back the van started and ran fine.
I reattached the engine cover, now sometime it still runs rough and it threw a po304 code, misfire of number 4 cylinder then ran fine and the light went out.
The van is also due for new plugs, wires, rotor and cap.
What should I be looking for to fix this problem when I do the plugs?

Make sure you use AC Delco spark plugs, distributor cap and rotor. Use good quality spark plug wires, Autolite Professional series or AC Delco. Put a dab of silicone dielectric grease on each terminal of the cap, inside and out. Don't forget the fuel and air filters. These items are a good start on a basic tune up. Most of the plugs can be easilly accessed through the wheel wells with the tires removed.