Chris
Not looking to hijack your thread but I'm having a misfire problem that might be the same as yours. I've been chasing this for months. Maybe some of this can help us figure this out.
This might be kind of long...
I have a '96 with auto trans. The ECU will give me a flashing CEL but only when the car is in park. Once the car is in gear the CEL will eventually stop flashing. It will also stop flashing if I turn on the AC and get the condenser fan to start.
My current theory

is that this might be fuel or injector related. On a fluke I noticed that the CEL will not flash if the gas tank is almost empty. I try not to let it run too low so I didn't notice it at first. Once I put more that a quarter of a tank in, the flashing CEL will come back.
I've read a lot of threads on other forums and looked at some service manuals to get an idea of how the fuel system works. If I have a leaking or stuck open injector the fuel may be bogging down that cylinder. When the tank is almost empty the fuel pressure at the rail may drop off slightly since the pump has to work harder. I geuss that shouldn't happen if the regulator is working right. When it goes down slightly, the engine can handle the air/fuel mix at idle. If the pressure goes up there is more fuel being put out by the bad injector especially in between spark firing cycles.
That could be why turning on the AC works temporally. The ECU opens the idle control valve to compensate for increased engine load from the condenser fan. The increased air and load helps to burn off the extra fuel in the cyl. When the car is moving the extra fuel can be burned without too much trouble.
Does any of this make any sense or am I completely off base about how the fuel system works?
I'm a little cautious in changing anyting else or buying a fuel pressure gauge since I've done that with no luck.
Chris have you noticed anything different with your fuel system?
I've changed, upgraded, or cleaned a bunch of things (plugs, wires, coil - also MSD, idle control motor, MAP, coolant temp sensor, throttle plate, etc...). Every time I reset the ECU, eventually it will come back to cyl. #4.
I thought about the ECU being a problem but it seems that that would cause a more random problem and not constantly come back only to the same cyl.