Don't replace with OEM. Get a PA Performance Alt from AM. But yeah, I'll bet that makes the code go away. Mine did the same thing.
In the market for a Fox body...
SOLD: 2007 Performance white GT Premium.
Performance: Eibach lowering kit, SVT wheels, Steeda Camber Casters, Steeda short throw, FRPP 4.10's, Airraid CAI, BBK 62mm TB, Brenspeed Detroit Rockers, Pypes Longtubes with O/R H and Violators.
For fun: Window louvers, 15% tint, Raxiom tinted taillights, J&L Audio sub.