Factory service manual has a thorough repair section- expected voltages, parts
locations, color schemo, all the good stuff. You're past the parts cannon phase.
Intermittent electrical problems in complex systems are some of the worst.

One thing I have noticed is that simply turning the temperature selector from cold to hot and back again is enough to get it cooling. The system has been flaky and I thought all the refrigerant had leaked out. I put the ac pro on it and the gauge still showed in the green. I probably have a slow leak, but maybe nothing major. Seems to be something else. When it cools, it will freeze you. When it works, it works well. Does this sound like the dash control unit?

As mentioned earlier in this thread, I would suspect either the control unit, or the HCV actuator, cable, or valve.
Pretty easy to check the HCV system. Cycle between hot/cold as you mention, and see if the HCV opens/closes consistently. You can look at the HCV on the engine bay firewall, or look at the actuator in the rear left corner of the passenger footwell.

The HCV actuator near the floorboard and the cable seem to operate freely when turning the knob from cold to hot. I cycled it several times and watched the operation. I also sprayed some dry lube on it too. I also saw the cable moving in the engine bay by the firewall and its operation matched the service manual. This all seemed to operate normally. How do you know if the HCV is working? I saw the cable moving, does that mean it’s working? Any other potential issues with it?

@jwkiss0 There will be a temperature difference inlet to outlet side of HCV when closed.
If not, HCV has internal issue. I/R temp gun a handy gizmo.

Hi there, Toyota has a TSB on a relay issue .
Not sure if you checked this?
My 2003 had a relay problem and the would work intermittently .
Relay turns compressor on. I put 1 in from a corolla and worked fine for a few years.

A/C light flashing?? Try this

This is a 3rd gen 4runner 1996-2002, the TSB for a 2003 4runner would be different.

The lines running in and out of the HCV all feel hot. Does this mean it’s faulty? Do I need a temp gun to see how close they are in temperature or should they feel different?

Just checked mine had 20-25* temp difference it not ideal troubleshooting at HCV due to heat sink.
Borrow one wouldn't buy one unless you just want too. FSM say's this pg. AC-63.

WATER VALVE ON-VEHICLE INSPECTION
1. WARM UP ENGINE
2. DISCONNECT WATER VALVE CONTROL CABLE
3. INSPECT WATER VALVE OPERATION
(a) Check that warm air blown out the vent when the water valve lever is moved to ”WARM” position.
(b) Check that cool air blown out when the water valve is moved to the ”COOL” position.
If operation is not as specified, replace the water valve.
4. CONNECT WATER VALVE CONTROL CABLE

Another quicky thing to check is the compressor clutch activation/solenoid.
- Just like checking the HCV, cycle the control between hot/cold.
- When set to cold, you should see the clutch engage the AC compressor on the engine.
- When set to hot, it should release.

Having said that, I've never looked at mine, and I'm not at my car right now. But, from experience on other cars, it goes like this:
- The AC compressor is run by a pulley/belt off the engine crank. (Engine front, lower, passenger side)
- Coaxial with, just in front of, the AC pulley is the AC clutch mechanism.
- When engaged, the clutch will compress against the pulley and engage the AC compressor.
- When disengaged, the clutch will release and spin independently of the pulley.
- The state of engaged/disengaged can be seen by watching that clutch plate.

These are just diagnostic steps before you start swapping parts or taking stuff apart.

hello i have an a.c. poblem on 2000 4 run ive tried everything ive read or watched except jumping from the low pressure relay behind glove box how is this done or is it worth it? just need clutch to enguage any info will be highly appreciated.

If the OP or anyone decides go for a climate control module rebuild, skip the $200 eBay guy - there is a guy on this forum, John Hadfield, in NJ who does (did) it for $63 including return shipping. Add $10 if you want new LED in diff colors.

Below is what he sent me about 6 months ago. My unit had lost its damn mind and did whatever it wanted to do. I got it back fast and it has been working flawlessly. The units are not hard to repair yourself if you can solder and know where the weak points on the circuit board are, but I was happy to have him do it while I worried about other stuff I've got going on....

"Right now, I am doing the repair for $63 which includes return shipping.
Shipping (TO John) usually around $10 to $15. If you would like a different method of return shipping just let me know.
If you want an LED upgrade, that's $10 more. Colors for the LEDs are
White, Blue, Red, Amber and Green and OE Green and ice blue. I have
examples of these colors if needed "