I checked the wiring and it all looked good before it started working, which was really weird. I guess there could be a control/signal wire that is shorted. I am still confused with it, because It wouldn't work at all. I'm pretty sure that it uses the resistor for the first 3 speeds, and reroutes through the relay for full speed and now it all works... so I just don't see how it could be shorted.

 

Does anyone have a wiring diagram, or know where that circuit grounds?

 

Which RPO? C40, C60 or C68? Refer to sticker inside of glove box. I will have it for 2001. Probably the same if RPO matches.

 

It is C60 (HVAC system, air conditioner FRT man controls)

 

here you go. this is for C60 but 2001

 

something as simple as a bad fuse? something has a small break and going over the bump, allowed the break to come back together.

 

Alright, the problem is now resolved. It had a bad ground. After fixing that it is working great all the time! I should have started by checking the wiring closer. Lesson learned.
Thanks everyone for your help! Problems all solved.