Hi Jason, I've looked at the Remy website and there are two alternators specified for your vehicle. DRA3296 - a four pin connector and DRA3545 - a two pin connector. These are engine number specific and it looks like you have been given the incorrect one. Looking at the wiring for them it is clear they are not interchangeable - that is, you can't wire one up to fit the other. The four pin has wiring for a control relay which the two pin does not.

The only thing I can suggest is to take it back and get the correct one as it is not suitable for your type of wiring. at least you know that the replacement you need is a DRA3545 (or equivalent manufacturer).

Hope this helps

Robin the Technician - I fix, therefore I am