You will be using the 01 computer. Drive by wire is ok and uses it's own module. You can use your 98 original harness. You'll just be adding some wires to the harness from the computer to the engine and extending some wires that are there now. It sounds hard but when you actually start doing it it's very easy. You'll be taking the pins out of your 98s computer connector and inserting them into the 01s computer connector. You won't be messing with any fuse boxes.
Pm lextech and he will email you the swap file. After you read that it will make way more sense