Seeing that it's a stock setup, is you CEL on or been on recently?
Other than that, do the basics. If you are driving this everyday, then verify coolant usage. The steam out of the exhaust will be noticeable different if it has coolant in it.
X2 on SSMonte, check fuel pressure along with vacuum.
Did you adjust the TPS when you put it on the new throttle body? How did you set the timing?