Contour Enthusiasts Group Archives Forums General Troubleshooting Random Misfire

Well, hopefully you also tried running without a chip first since you are running the stock MAF and injectors right? If it has the same problem with stock code and it is misfiring then I'd look again at the ignition wires,coil, plugs, connections.

I would look at the connection to the coil pack where the four conductor plug is at. Make sure there is no corrosion, it fits tight and has the rubber seal. PCM plug can have a problem.
Corrosion problems are almost always affected by temperature too in my experience.
Last would be to test with good stock style plugs and wires.

I'm sure you'd get a crank or cam shaft sensor code, but there could be potential issues there.