Okay, I'm going to answer my own question...
Turns out swapping a '99 Cobra cluster into a '00+ car is NOT a direct swap (for the most part). You can use the gauges, but you need to swap out the large circuit board on the back.
For some reason there is some wiring that goes through the cluster for the rear defrost. On the cars with the defrost button down by the shifter it's the yellow wire with black stripe that goes from the defrost switch into the cluster. Out of the cluster is a black with yellow stripe that goes to the defrost relay.
On the '99 Cobra cluster I had these two wires were unused and connected to ground on the PCB causing the rear defrost to stay on all the time (even with the key off). It also caused the rear defrost fuse to blow under the dash.
The post '99 clusters have some sort of logic circuit in the cluster board that controls the rear defrost. I don't know why though. Maybe the defrost timer is integrated into the cluster on the newer cars. I compared both large circuit boards side-by-side and there are significant differences for these two rear-defrost wires. It's not a simple wiring change.
So, if you want to use a '99 Cobra cluster in a car with the defrost button by the shifter ('00+ I think) you can either:
1) Swap the odometer board AND main circuit board from your original cluster to the Cobra one (ideal)
or
2) Pull the wires at position 9 and 10 (yellow/black and black/yellow) out of the left harness and this will disable the rear defrost.
Riley