You might check to see if you have plenty of clearance between the core support and the engine and trans. I have seen alot of neons that have bottomed out at some time or another and pushed the core support back into the engine of trans. Especially the second gen cars. The The PCM and rad fans like to come in contact with the trans causing the issue you describe. One other thing, Have you ever done a compression test on your engine? Later 2.0s had horrible valve jobs and are common for the valves not to seat well and cause miss or shake without setting a MIL.