Based on your description of the installation (unit now piggybacking ECU, new injector, just purchased), I am 99% sure that you have the Uni-T or Unichip. Since I just ordered the same setup, I would say that you went from the original 3.0 inch (4.5 lb) pulley to the 2.8 inch (6 lb) pulley.
I would imagine that will pick up significant power by switching to the uni-T and the smaller pulley. You should be able to go a 6or 7 psi with the intercooler.
Have you tried actually taking the bulb out of the check engine light on the back of the instrument gauge? I understand that you want to rid yourself of the actual issue...but as they say "out of sight, out of mind"
Also, have you called TPC lately to confirm the uni-chip price? $2,500 seems $1,000 high to me.