P0303- Cylinder 3 Misfire
 

So I just got done doing the gaskets on my lower intake manifold, and replacing the timing cover. I had some issues putting the distributor back in, and I was sure I was off a tooth because the engine was running really rough. This is when the P0303 code showed up. I ended up taking it in to a nearby shop to see if they could get to the bottom of the code. Supposedly, they put in the distributor correctly, but it still had the misfire. They claimed it was because spark plug number 3 probably was burnt out. They also said my spark plug wires were fine. I ended up replacing this spark plug, but the misfire was still present. I replaced my rotor and distributor cap as well (cap contact points looked to be pretty corroded), but the misfire is still there as well as the code. What else could be causing this misfire, and how can I diagnose these?

Double check that the plug wires aren't crossed. There are two of them (1 and 3?) that don't go the way they look like they would.

What Tom said above. Then.......

Check cam sensor retard with a capable scanner and report. Should be 0 degrees +/- 2 degrees.

Are you sure that you have a felt misfire? Crank sensor relearn should be done after timing cover replacement, and not doing it could cause a P0303 - but this would not cause an actual felt misfire.