Fuel Ijection problem

[76cruiser]

I fitted a T.R.E to my 99 Hayabusa and it ran sweet, the throttle was smooth and it seemed to have better acceleration but the FI light wouldn't go out. I then discovered that I had plugged T.R.E into the FI wiring by mistake. I then found the correct plug and changed it. The light went out but now the engine doesn't have that smoothness anymore. Would it harm the fuel injection if I put the T.R.E back into the FI connection?

 

[Lucid]

I think it's safe to say that most on here don't recommend using TRE. I'd take it off and get a dyno tune to manage the timing retard per gear, and also smooth out your motor.