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It appears that my computer is bad, possibly due to battery acid leaking onto the harness. The Thunder Racing guys have looked at everything possible that would cause the problems, and everything checks out OK. They have LS1 Edit but can't do initial programming of a new chip.
It looks like I have to have the dealership put in the new computer with stock programming, then have the TR guys use the LS1 Edit in order to work with my many mods.
Have any of you had this problem? Any suggestions?