I have a 98 Sunfire with the 2.2 SFI that has a horrible rod knock. I also have a 2000 Cavalier with the same motor but the head is junk. Is there anything stopping me from putting the 98 head on the 2000 bottom end? Is there anything different between the motors? I can visually see that the 1998 has an EGR valve on the back side of the head on the transmission side of the motor but the 2000 doesn't. Is anything else different? Any help would be greatly appreciated.

They're different motors. I don't know how much can be swapped, but it's limited.