computer is diffrent, might need to swap the 2000 computer from an auto computer to a 6sp computer. Don't recomend using the e99 computer, later ones are tuned better from the factory. I have an early 99 6sp, and would like to swap out the computer to a later one... but the hard parts, pedals, steering column, trans and transfer case parts should all interchange fine, as far as I know.
I spoke to a guy that had a 2003 that came with an auto (rare, it was 5R110, only availble in the 2003 year trucks from what he said, I had thought they only came behind the 6.0 motors, he said he bought it new, and it was an option, 4R100 or 5R110 trans, and 7.3 or 6.0 motor) After he swapped in the 6 sp trans, it ran ok, but had a dead spot at times, had the computer re-burned for a 6 sp truck, and it runs fine now. Food for thought, keep the computer issue in mind.