When your "check engine" light comes on... does it remain on for the duration or does it come and go following any particular pattern?
Also, when you're seeing the CEL, the ECU logs an error code. If you ask your dealer what error codes they've found and report back, I may be able to shed a little light on what's pissing the ECU off.....
You dont have to completely disconnect the exhaust flapper loom plug to trip an error code.... if the actuator cable is incorrectly adjusted you'll also get the CEL come on at start up. But this is only one of a myriad of possibilities... and something any half competent dealer ought be able to resolve pretty quickly.
and termis put on with remapping.
Remapping? If you bought a Termi kit it would have come with a remapped "racing" ECU. Do you still have the stock ECU?