I bought an electric fan harness for my 05+ fans and it has a blue pin connector and a green pin connector,idk which one is which because most of the write ups on how to install them have one the green wire to pin 42 and I know since I have two one goes to pin 33 and I'm guessing that that pin on the PCM isn't unused like pin 42

 

I have no idea what you're saying, perhaps punctuation is not your friend.

This is what I see: you have a 2000 truck and an 05+ harness with the factory blue and green PCM wires. If so, the green wire will go to the Blue 42 PCM pin. The blue wire would go to the Red 33 PCM pin. I do not know if the Red 33 pin will work for Fan 2 on a 2000 model. Someone else can verify this. I would go ahead and hook it up, make the change in HP tuners and test it out.

Post of pic of exactly what you are talking about if my understanding is incorrect.

 

I take you have a 2000,if you purchased a aftermarket fan harness, such as a blackbear or from ls1fans.com, the blue pin goes into pin 42 of the pcm, and the other wire goes to the green wire for your a/c relay, if you have a 05 pcm, then you just install the pins directly into the pcm, also don't forget you'll need a custom tune to activate the pin in the pcm.....