You realize that if you put the 2003 ECU in, you have to have the Security keys from your 2000 programmed into the 2003 ECU, right? The systems should be the same, but if you ECU doesn't know your 2003 keys, you're out of luck. Probably the simplest is to drive the car to the dealership with the 2000 ECU and a fully charged battery, then put in the 2003 ECU and ask them to program the keys in.
Your other option is to ship the 2003 ecu to American Motorsport (see the EEC forum) and have him just disable the security.
-Dan