Each gear has an individual solenoid, so yes, a single faulty solenoid can prevent a single gear from engaging. I dont know what the process is to do this on the Aisin unit in your 4runner, but Ive replaced solenoids on a ZF trans on my BMW xDrive wagon . . . some skill and problem solving required, though not an awful job. I too have a lift in my garage, which reduces a significant amount of brain damage.

I would check codes in the TCM, then ECT/TPS sensors, then look at fluid. It sounds like you are going to replace fluid, so might as well see if any of the other items are shot, then go on to the fluid. Maybe check and see if you can drop the valve body that holds the solenoids (or however it is on the Aisin) and if its easy/cheap, give it a go.