just changed out the head unit in my 01 gs, and found out after everything was put back together that my remote, alarm, clock, and homelink setup all no longer function. Has anyone else ever encountered this problem, or have any idea what I might have done to mess everything up? btw, I had the pioneer system stock.

 

welcome to CL....

your going to find more info in the audio forum and if you do a search there.
https://www.clublexus.com/forums/lexus-audio-video-security-and-electronics-12/

you should first check your fuses then take it from there.

 

smells like blown fuse to me.

 

Yes, check the fuses. Also note that there is a fuse panel on the passenger side as well. I totally overlooked this panel last time and thought I fried the circuit cause I couldn't find a blown fuse in the other two panels. I'm almost certain it's a fuse in the passenger panel.