When the dealer told me I could not have the Digital A/C or the cladding in the 5-speed (5-speed was 'must have') SR5 edition of the 4Runner, I said: "You made my day, I don't want either one. The cladding is ugly and the digital control is less reliable." The only thing I liked in the Limited were the painted bumpers instead of chrome.
This thread is confusing the OP's question with the difference between the Automatic and Manual HVAC systems. The pictured control is the '01-'02 version of the MANUAL HVAC control, wire diagram attached.
This '01-'02 "manual" system is far more automated than the '99 MANUAL HVAC and includes THREE servo motors for Air mix, Air Inlet, and Air mode control. All three of these systems are completely mechanical on the '99 Manual system which has ZERO servo motors in the system. Thus, besides having to add the three servos, the A/C amplifier is wildly different and would have to be changed. I have the '99 EWD in paper so I am confident in what I am saying. The A12 plug on the A/C amplifier in '01-'02 "manual" system has 25 wires on it. The same A12 A/C amplifier plug in 1999 has only ten wires, mainly due to those missing servos.
In my opinion, that upgrade would be a massive and expensive ($5000+) undertaking to do from new parts. Even with a full donor truck, however, I doubt it could be done, requiring three servos, head control, A/C amplifier, and the HVAC wiring harness at a minimum. In addition, looking at the parts lists, EVERYTHING changes as of July 2000 when the '01 model came in. Cooler unit assembly, heater box, blower unit, basically EVERYTHING inside the firewall. So non-starter in my book. There may even be sheet metal changes to accommodate the changed components--no way to tell.