On a 2002 Cadillac Seville SLS Can you replace the wiring harness that runs from the fuse box to the alternator or do I have to replace the whole engine harness?

You may very well be able to obtain the shorter harness. Or a wiring connector which would allow you to repair the wires. I'd see a parts store or dealership parts department to ask specifically - and see how you do. Use this link to find some shops near you that can help with your concern: www.repairpal.com/repair-shops