Do you have the manual or the auto control with the digital readout? (I think SR5's had both in '99, don't know about your year). I don't think either one uses vacuum for any control function. The manuals are all levers, cables and plastic gears (which can strip and jump off their centers) and the autos use electric servos for mix and temp. I'm no expert, but that's how it looked when I went through that part of my FSM.
The autos have a self-diagnostic routine that puts trouble codes on the Temp read-out, probably a bum servo. If it's a manual, just get in there and trace the linkage from the mix control to the mix flap.