After re-reading this entire thread I think your next step is to set aside some time and really check out the entire harness. I think you mentioned an aftermarket alarm? If so, locate that and all associated wiring and check it over very well. Could be that one of more of the connections from the aftermarket alarm to the factory harness are failing and causing shorts or other odd behavior.
It sounds like there are too many different issues going on (long term code, misfire, brake light issue, turn signal issues) to be able to point to one specific cause (other than a harness issue).
- Justin
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1999 Camry - Beigemobile DD
2002 Suburban - Wife's DD
2004 Grand Cherokee - Not running / Project / Selling?
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