Probably need new plugs to start off with (NGK# DCPR9EIX are Great). A TPS reset can't hurt it, followed up by a nice long cruise (Learn-in Ride) holding a steady 3000+ RPM. And the ECM tuning is the Best thing you could do to maximize performance from the mods that you've done.
Edit: You may consider throwing in some good high octane gas or even adding Seafoam to pep up the winter gas.