It is the stock wiring harness actually, we held onto everything that came with the original head unit including both plugs that go into it in case this ever happened, the only mistake we made was not marking them. the green and blues are the exact same color, and the two yellows are obviously the same color cause the wire diagram that is used for this car uses the yellows twice. But, that wire diagram is generally for after market head units, no? I'm going to attach a picture of the wiring. I have them all wired up, for safety purposes, I haven't tried powering it up yet cause I don't want a electrical fire because of the yellow being a 12V+.
No way that's stock, I can't imagine why it wouldn't be, but I just want to see that's some sort of rewire. Those wires are too clean and none of them have any marks on them. I also have a 98, as does my friend, and I've put radios in a variety a GP and none of them looked like that.
As I recall, your colors should be orange for the constant "trickle" 12v
yellow for the switch 12v power wire
brown for the illumination
gray for the dimmer
tan and gray for front left +/- respectively
light and dark green for front right +/- respectively
brown and yellow for rear left +/- respectively
dark and light blue for rear right +/- respectively
as an SE you MIGHT have an antenna too in which case you'll have a pink wire.
Some of the slots in the harness should be empty.
For future reference, any time you meet someone that's cut stock radio wires, slap them upside the ****ing head as hard as you can.
edit: here's the diagram from the12volt.com, appears i'm correct on that,
1998 Pontiac Grand Prix Stereo Wiring Information
either GM made a joke with your car, or someone rewired it.
edit2: for the power wires, just usage a voltage meter to test them, car off one should be constantly powered, the other should receive power with key-on, the speakers mixing them up shouldnt be a big deal, but you can easily do guess-and-check with those.