If motor runs on constant speed but airflow changes I would suggest broken level or linkage to one of airflaps. Such flap just 'sets' self simply by flowing air at random positions.

Yeah all of the positions work when it's working, I replaced all the parts with brand new parts. I have a blower relay I'm going to replace today but yesterday after writing this, the problem never happened again for the next 50 miles I drove it.

This kind of makes the most sense, how big of a pain in the ass would this be to inspect and repair? The whole dash has to come off right?

Thank you for this reference. I've been getting skunked searching for the resistor in my '86 4Runner.

I am having a similar issue with my heater blower except it isn't the resistor or fuses. All the sliders work except for the actual blower one. It worked before but feels like the mechanism has snapped inside as it is really loose now and just flaps side to side without any resistance or doing anything. I have taken the full dash off and can see it connects to a yellow module which I want to replace but I can't figure out how to get it out as there isn't enough space behind the module to unclip the connector and then I can't move the whole until forward that houses the other sliders. Anyone have any advice would be greatly appreciated. Cheers

Finally got the part off. It's got 415 1012 written on the side but can't find one online with that part number. Anyone parting their 4runner that would have one or know where I could buy one. Thanks

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This sounds similar to an issue i'm having with my 2000 T4R with the manual AC unit with the 4 speed blower fan switch slider. I had to wiggle it to stay on, but now doesn't turn on at all. I replaced the blower resistor thinking that was the issue, but the issue remains.

I took off the center console and looks like the piece the lever is attached to is broken, the lever is kinda drooping. If i push up on it with my finger, it tuns on. The part looks similar to the picture you posted above. Not sure if I can just replaced that part or if i need to replace the entire AC unit. Found tons of used units on eBay but since these manual units have cables to the recirc vents and another cable for the hot/cold knob that pulls the cable that opens/closes the heater control valve. I've yet to find a DIY on replacing these manual AC units

Here's a video of the issue:
2000 3rd Gen 4runner manual climate control - YouTube