To get the codes read, you could take it to a repair facilty, which may charge you $40-$60, but that would be better than changing a $200 EGR valve you don't need.
Did you swap out the PROM chips from your old ECM to the new one, or did you install it as-is from the donor vehicle? If you didn't swap the PROM, that is probably most of your issue as each PROM is calibrated to that specific vehicle.
Finally, the 3.4 DOHC's are known for intake leaks that only affect operation when cold. As the weather gets colder, the metal shrinks more, causing gaps that the intake gakets can't keep sealed. As the engine warms up, everything expands and the engine will run better.