2000 Taurus new motor wont run security?

Just put a 2003 motor and tranny in a 2000 taurus SE, if you try to start the car the security light comes on and nothing happens, I am using the computer from the 03. If I put the original computer from the 2000, the car start right up and runs good but the car will not charge. Can I reprogram the 03 computer to work in an 00? Thanks for any ifo you may have.