HELP! Trans light on (back up mode?)

I'm having a problem with a 1995 Trooper. I changed the plug wires and after that the transmission light started blinking. The manual says it's in back-up mode, so to drive it you have to shift gears manually. Took it to Mr. Transmission and the said it's internal. Then took it to another reputable transmission shop and they said the computer put out over 35 different codes and also said the problem most likely was in the wiring somewhere. Should I take it to the dealer and get reamed? Anybody have any suggestion?????