Well, everyone must still be out racing........
The 16bit 99-2000 stator, and 32bit 2001-2007 are different. The 16 bit stator has long ridges with gaps in the middle. The 32 bit stator has lots of notches or teeth. It defines the crank sensor pulses, and coordinates with the ECU for timing advance and coordination.
If you bolted the 07' in, and didn't change your stator it is simply not keeping tempo with the factory FI mapping. Then again, there are differences in camshaft profiles, and timing/fueling related data in the map for an 07' that are different for a 99-00'.
You might want to seek out an 07' ECU, and wiring harness so the entire group is correctly matched. I'm a bit tired, but I know there's more to the picture here. Not a lot, just trying to remember what one needed over the other.
If you're spinning an 07' stator, and timing sensor on a 99-00 ECU, it's not working as it should.
Simple fix. Just build the 07' fuel injection system up to par with the goodies mentioned, and all should straighten right out.
A.