Intermittent miss in ignition??

I have a '95 Mazda Millenia with the 2.5 L engine. The car quit on me recently and so I took the front of the engine apart to see if the timing belt had snapped. What I found was that a piece of the timing cover had gotten caught and run between the timing belt and the crankshaft skipping it 9 teeth. I retimed it and put the whole thing back together and now I have an intermittent miss in my ignition. The problem is, it's not on a cycle. It seems to get worse as the car gets hot, and I already tried replacing the plug wires thinking I had some problem with the plug wire resistance getting too high as the car got hot. (I had the plug wires and plugs removed while doing the maintinece so that I could turn the crankshaft with no compression.)

I cannot think of anything else it could be unless my distributor or one of my plugs is bad, but it seems like both of those things would be bad on every cycle (i.e. I would just be running on 5 cylinders). My problem is that the car runs fine most of the time and just occassionally skips on one cylinder. Any ideas?