Sounds like a wiring harness, but I work aircraft, not cars. The PCM could be on it's way out (big $$) but it's most likely something electrical as there are just way too many problems there.
IIRC, the ATX trannies have a 4000 rpm limit in neutral or park BTW. Otherwise your limiter should be at 6750 but I can't see an ATX hitting that mark with a speed limiter of 112mph.
