The alternator is correct for the car, with the original harness and voltage regulator. To work properly, all the wires would have to be connected as the factory had them. You can't do that with the replacement harness you have without modifying it. Since alternators are cheaper than harnesses and the 10SI will bolt right in, it's the easy-good fix.

Without seeing what you had before you replaced the wiring, it's hard to tell what was wrong. I've worked on cars that had some incredible workarounds done that worked somewhat, but never quite right.