Bosch and Valeo make alternators that fit the NA and the SRT without any modification. They come with the correct pulley and the correct connection to the appropriate loom.
If I recall correctly the shaft on the NA version is shorter than the SRT version and the electrical connection is different as you have found.
I have a chart on here somewhere that gives the Valeo numbers for the alternators and the Bosch number that it replaces.
I suspect the alternator you are replacing is not the correct one and the pulley on it did not fit properly.
Click on the index ..... In my signature and look for the chart in the Engine-Electrical listing.