Okay, Nevada's comment about a knob behind the glovebox kept throwing me off because there is no adjustment shown in the wiring diagram. An older co-worker mentioned to me that there is a manual adjustment for the expansion valve on older 4Runners which is what I assume Nevada is talking about. Which got me thinking along the lines of pressure, so I leaning on a mechanical issue with the compressor and/or expansion valve.
Nevada, could you post your trucks model year & trim and a picture of where this knob is? Our FSM doesn't show anything like that for the 3rd gens.
As for your repair order Ryan, that is a weird list of parts, I can understand why they would replace the fan clutch, believing that a lack of proper airflow over the condenser could cause a lack of proper cooling at low engine speeds. But when you brought it back for the same problem they should have started looking at the compressor clutch, unit, and possibly expansion valve.
I think HarleyDoc may be onto something there with the expansion valve, they rarely go bad, but it could cause some issues if coupled with a failing compressor with inconsistent pressure. I honestly think the fix for your car is a remanufactuered/new OEM compressor w/ clutch, expansion valve, and if you can afford it I would go ahead an replace the reciever/dryer. (was this ever replaced when you converted to R134A? Most shops don't do it, but technically you're supposed to since the refrigerent and oil tends to pool in there.