Now the blades track fairly even but the heli wants to pitch right (even with full trim to left). It does not fly as stable as it did before either requiring much more correction even to hover. It did not do this before the upgrades so I don't know what is wrong.
With all the stuff you replaced, it could be that the swash plate isn't level anymore. First I would eyeball it, is it perpendicular to the shaft?
Here are instructions for getting it leveled out:
http://www.rcgroups.com/forums/showthread.php?t=642401