I have a 1998 4-Runner. The air conditioner is not working. Freon level is fine & compressor kicks on & blows ice cold when you run power directly to the compressor. Electric door locks now only work when ignition is on & 30 second delay to use windows after ignition switch off is no longer working. Recently had starter changed. Problems occurred since then. Could use some advice on how to proceed. Thanks, Rick

Hey Rick..... Although I have never personally come across all of these problems combined at one time I was looking over wiring the wiring diagrams for each system you mentioned.... A/C, locks, and windows and found the only real major thing they share is use of the Integration Relay.

Its basically a box of several relays combined into one which hugs the fuse box. A google search can pinpoint what it looks like and such a bit better.

I'm assuming that you've checked fuses and the like. Figured I'd try to lend a hand. I've seen these cause all sorts of odd combinations of problems and it is one of the only links between the systems you mentioned. I'm not positive that will fix it being with all the unknowns like if anything was messed up during the last repairs and whatnot but again just trying to help get the ball rolling.

Welcome to T4R !
I moved your post to the 3rd gen section, maybe someone has encountered your problem before.