What about on the '01 & '02 models? My '02 Tacoma had manual controls that looked the same as the manual controls on the '01/'02 4Runner, and there were no levers, just electrical connections.
EWD for an '02 manual HVAC:
http://tacoma.site40.net/4Runner_96-02_Repair&Wiring/techinfo.toyota.com/ileaf/ewdtmc2/ewdtmpdf/ewdsourc/2002/024runne/systemci/057acman.pdf
and for the digital:
http://tacoma.site40.net/4Runner_96-02_Repair&Wiring/techinfo.toyota.com/ileaf/ewdtmc2/ewdtmpdf/ewdsourc/2002/024runne/systemci/056aac.pdf
You're absolutely right, the differences are far fewer than the earlier years I had looked at the last time I answered this question. I had no idea the '01-'02 were like that. The plug numbers on the servos, the blower motor and the thermistor are the same; it looks like those would just plug up. You would need a resistor in place of the linear controller on the blower. The control amplifier plugs are totally different. The manual uses a single 25 pin plug, the auto uses two--one 26-pin and one 16 pin. Now, if you had the control, amplifier and harness from a manual and plugged in the three servos, you would have most of a system. You'd need to make about ten new truckside connections to the manual harness, two power wires, a/c clutch, ECM, and heater relay. Some of these would be a pain, but doable.
Would it work? I think so, but no guarantees. But yeah, If I wanted it badly enough, this I could do.
The big issue is the harness. Those wires dive directly into the the truck harness; it's not like an engine where it's a separate thing you can yank out.
The other option is trying to cut and splice the manual plug on to the auto harness. The more I think about it, that is probably the way to go. 25 splices and some rewiring elsewhere on the truck, including installing the blower resistor. Most of the colors would match. Not for the faint of heart, but doable.
Please don't ask me if you could put an '02 manual control on a '99 auto system. But....maybe.
EDIT: Crap. OP has a 2000. I'll look at it later.