I just recently had this issue. Today I was able to successfully fully repair the issue and all functionality is restored. It is a total pain in the arse, took about 12 hours. Thankfully I have 60/40 split bench.
1. Remove lower cover in the center hump (two plastic screws each side)
2. Remove drivers kick plate (one plastic screw at the carpet meeting point)
3. Remove drivers sillplate (pull up)
3. Remove lower dash panel (two bolts either side in the lower corners)
4. Pull the lower dash from the mounting (disconnect all wiring)
5. Remove the knee airbag assembly (four bolts and a wire harness) harness has a black clip that must be pried gently upward to remove the plug.
6. Remove the OBD II port from the lower dash panel
7. Remove parking brake from lower dash panel
8. Remove light from lower dash panel and set panel aside
9. Remove drivers foot duct (one bolt under where the airbag was attached to the brake assembly bracket) now gently pull the duct from the heating unit
10. Remove the gas pedal (two nuts and one wire harness) set aside
11. Remove cubby hole in the center dash (pull outward)
12. Pull the carpet back (two pieces of velcro at the top (be careful here you can easily pull the staples out the velcro)
13. Remove the exposed structural brace bolt (bottom of brace) this is the brace next to the heater box
14. Remove the foot heater duct piece that is still attached to the heater (piece where the duct was removed from early) two screws
15. To the hard part, remove the drivers servo assembly (four screws top and bottom center and left and right center)
16. For the screw behind the structural support its easiest to drill a hole in the support to remove it unless you have specialty tools you can get it out. (I removed mine with a micro ratcheting driver and later drilled a hole to reinstall it) Careful when drilling its easy to push right into the servo plate and heater box
17. Remove the servo wiring (also very tedious)
18. Maneuver the servo plate off the heater assembly
19. Once the servo plate is removed inspect for damaged gears and the like (mine was fine and the jamming was likely caused by accessory wires that I found caught up in the gears and caused the gear to become off by a few teeth)
20. On the backside of the servo plate there are two large gears with a gap in there teeth those gapped teeth need to be meshed in order to have everything in sync for reinstallation. Also there is two alignment holes in the servo plate and the upper white gear. (The servos cant be turned by hand use on of the plugs in vehicle to align the servo plate servos) If your lucky these are already in alignment if not it'll take some trial and error (your shooting to have the gapped gear areas meshed together and the alignment holes in the servo plate line up with the white gear holes.
21. Next is the black gear on the servo plate (also has a big tooth) this tooth aligns with triangular gear on the heater (this triangular gear has a hole in it for matching up with the servo plate alignment holes.
This is where is gets ready tedious and lots of curse words were used.
22. There is a diagram for setting the flaps in the proper orientation in the service manual I'll see if I can post if when I'm done, push the upper most linkage (defrost I think?) at the bottom of the linkage clockwise (this should raise the linkage) you want it all the way up and you'll need something to hold it in place (I used a jewelers screwdriver to wedge between the forward shaft and the heater forward wall to hold it into position)
23. The next linkage down needs to be rotated all the way so the small triangular gear at the top move towards the passenger compartment, again line up their big teeth (should have alignment paint on them as well) you may need to push the upper cog (it moves via the servo plate white gear channel so its somewhat independent to the movement with the plate removed) up first in order to do this as sometimes it prevents the linkage from swinging up easily (rotation is counter clockwise).
24. Prepare to reinstall the servo plate onto the heater. (I tired about 30-40 times and only got it once) don't make the mistake I made and run the air conditioning alignment in Techstream it screws up the gear alignment if you have manual A/C controls like I do, I don't know if it works for the auto climate or not.
**Note its much easier to remove the bottom servo from the servo plate and install the black gear onto the heater side (again align the big teeth and slide the black gear onto the resting position (circular hole toward the engine bay in front of the triangular gear).
25. Optional if you are performing the reinstallation with the black gear on the heater side, remove the lower servo (be careful you can easily break the little clip that holds the servo on the white gear.
26. Optional Remove the black gear and place it on the heater side as mentioned above
27. Optional Remove the two screws holding the lower servo to the servo plate
28. Optional pry the clip on the back of the servo plate holding the servo to the white gear and remove the lower servo.
29. Reinstall the servo plate, the lower flapper needs to be all the way down (I just held this as I reistalled but you can use a rubber band to hold it as well) you also need to use a screw driver, punch or drift pin to put through the alignment hole in the servo plate, white gears, the large triangular gear and heater box hole to ensure proper alignment.
30. If you have DC (like me or a CM) there is the gears for the rear vents all the way at the bottom toward the passenger compartment (little round gear and a medium triangular gear. There is no alignment diagram for them and they do not get aligned with there big teeth lined up, mine was aligned somewhere towards the bottom center. (you'll just have to trial and error this, took me about 10 tries) you'll know this is out of alignment when the controls allow movement in one direction and then it binds trying to go back (you'll be stuck in defrost only again).
31. Allot of trail and error but once the plate is on or you think your good remove all the things you used to hold the upper and lower linkage in position if used
32. Optional if you removed the lower servo reinstall it now, you'll need to use the servo plug to turn the servo shaft so the flat portion is straight up and down to install. If the black gear isn't straight up and down make sure it stay meshed with triangular by keeping pressure on the servo plate and rotate by hand or needle nose pliers until it is straight up and down with the flat section for insertion of the servo. Ensure the other servo isn't plugged in or you'll mess up the alignment and have to start over.
**Note the lower servo needs to have the flat piece straight up and down for proper alignment with the black gear if your removing it. Weather or not you remove the lower servo to make the reinstallation easier you likely need to remove it to align the servo plate gearing anyway, use the servo plugs to turn and align the servos and gears dont plug the plug in all the way as you need to quickly remove the plug/s when the gears line up properly (It's also easier to remove the servos align the gears and then individually plug in just a servo to align its shaft for reinsertion into the servo plate.) You likely have a 45-60 second delay until you can control the servos, dont worry this will go away once everything is aligned and installed properly.
33. Install the top screw, bottom screw and 1 middle screw once the servo plate is installed (leave the rear passenger compartment side middle screw out) this the screw that you likely drilled a hole in the support to remove earlier.
34. Connect up the servos to the harness and test
35. If you have binding its most likely in the lower linkage that controls air flow to the rear passengers (you can get lucky and slightly pry towards drivers side of the servo plate away from the heater side while trying to move this linkage into alignment. (you can also see the alignment peg through the area where the cubby was removed earlier but not well). This is how I finally found what alignment I needed (do your self a favor now and take a sharpie and make alignment marks for the future.
36. If no binding and full operation is restored your done, otherwise remove the servo plate and realign and try again.
37. Once eveything is working reinstall everything previously removed in reverse order.
**Note everything I removed doesnt have to be taken off but you'll thank yourself in the end if you remove it first, I didn't but later did because there just isn't any room to work or see what your working on.
Took me a total of 12 hours to do this, but Toyota will charge in excess of $2k for this same work if they will even attempt it.
Also the servos rarely go bad but are just bound up by the gears so dont freak out if there is zero movement clear the bind and you'll likely be good.
**Note before testing I recommend checking for slight play in all the meshing assemblies before doing and operational test it can speed the process as if it binds you'll likely have to remove everything and realign it again. If you dont have a little play it will likely bind to play with the servo plate alignment before testing so you only have to adjust the gearing on the heater box to mesh properly with the servo plate and not realign the servo plate now.
Happy Head banging!! If your like me you'll be an expert at this when your done, but hopefully this will save someone some time and an expensive trip to the dealer.