BLKNBLU
Explorer
Here is a what and why about the air flow meter adjustment.
http://www.4x4wire.com/toyota/minutemods/afm/
Essentially the same thing from Downey
http://www.downeyoff-road.com/EngineComponents/FuelInjection.html
More AFM tech from Roger
http://www.4crawler.com/4x4/CheapTricks/AFM/index.shtml
Specs on the different TRD cams
http://www.4crawler.com/4x4/CheapTricks/EngineMods/index.shtml#CamSpecs
If you still have contact with the guys that did the work, see if you can determine which cam they put in. Also if they tweaked the throttle body. Generally the mild cams don't require any adjustment. I have one from a different company but essentially a level 2 cam that I run with LCE headers, stock TB, and no adjustment of the AFM. Perhaps if you have cam/headers/and TB mods all together that added up to the need for AFM adjustment?
On the gearing, conventional wisdom is that 4.88 is the perfect match for 33's. Take that with a grain of salt. I'm now sas'd with 35's and 5.29s which is supposed to be the optimal pairing. What I have found though is that I'm running a little under the speedo when compared to GPS (about 10%ish) So I figure I may be able to fix that with 37's, but that is going to have to wait until the current tires wear out and that is going to be a while. I ran my 4.10s with 31's for years and had the same situation as you, 3rd gear to get up the long hills. But the only time I had temp issues was when my rad was on it's way out. On the other hand I was carrying nowhere near the weight as you. 4.88s with 31's should have you zipping up the hills but the engine will be screaming from high revs.
http://www.4x4wire.com/toyota/minutemods/afm/
Essentially the same thing from Downey
http://www.downeyoff-road.com/EngineComponents/FuelInjection.html
More AFM tech from Roger
http://www.4crawler.com/4x4/CheapTricks/AFM/index.shtml
Specs on the different TRD cams
http://www.4crawler.com/4x4/CheapTricks/EngineMods/index.shtml#CamSpecs
If you still have contact with the guys that did the work, see if you can determine which cam they put in. Also if they tweaked the throttle body. Generally the mild cams don't require any adjustment. I have one from a different company but essentially a level 2 cam that I run with LCE headers, stock TB, and no adjustment of the AFM. Perhaps if you have cam/headers/and TB mods all together that added up to the need for AFM adjustment?
On the gearing, conventional wisdom is that 4.88 is the perfect match for 33's. Take that with a grain of salt. I'm now sas'd with 35's and 5.29s which is supposed to be the optimal pairing. What I have found though is that I'm running a little under the speedo when compared to GPS (about 10%ish) So I figure I may be able to fix that with 37's, but that is going to have to wait until the current tires wear out and that is going to be a while. I ran my 4.10s with 31's for years and had the same situation as you, 3rd gear to get up the long hills. But the only time I had temp issues was when my rad was on it's way out. On the other hand I was carrying nowhere near the weight as you. 4.88s with 31's should have you zipping up the hills but the engine will be screaming from high revs.