I am looking to replace the center console with one from a newer model. Are there any differences in the 2002/03/04 vs the 2000 console, aside from the cup holders (the goal) and the shifter trim plate? If I find one in a junk yard will I be set?

yes the 00-01 consoles SUCK

you will need the parts from a 02-05

you will need the cup holder section, the shifter trim plate and the, piece that goes under the climate controll to relocate your Traction controll switch and heated seat switches ( if equipped)