I just replaced the cap and rotor on the distributor and it runs fine, except when I come to a stop the engine stumbles once and the check engine loght comes on, but it seems to be running fine still. I can turn the engine off and back on and the light will not be on. I drive it a while and then when I come to a stop it does it again. Sometimes this won't happen. Maybe about 2/3 of the time. Suggestions on what it might be?

 

Pull the code and see what the CEL is on for. It could be something completely unrelated to what you just replaced.

 

OK, pulled the code and got a 9 No. 1 Cylinder Position Sensor. What exactly is this for?

 

This is one of the sensors in the distributor. It synchronizes the fuel injectors to the rotation of the engine by telling the ECU it is time to turn on injector 1 just as the intake valve of cylinder 1 opens.

First make sure the plastic insulator plate that separates the high voltage section (cap and rotor area) from the rest of the distributor is in place. Check the 8 wire plug to the distributor being properly connected. There is a procedure to check the sensors with an ohmmeter in the service manual.