I have a 2003 Bonneville, will an 4t65e from a 2000 work in a 2003, is there any differences between years?

Yes there are differences in years and no an 03 probably won't work in an 00. Reason being is they made quite a few changes with external vs internal pnp switches etc. 03 was different. I can't remember if there was a seperate tcm to control it or not.