I've had hesitation issues since I bought the truck. 4 runner 89 4wd. 22 re, EFI...Over the years here is what I did since. i always had hesitation. I think I finally figured it out.
it ran good, but on rainy days and sometimes not, it would bog down and throttle would jack around 2-3k RPM in gears 1-2. You would have to gun it to force it through.

1. Change air box to K and N cone filter.
2. change plugs wires. cap and rotor
3. fuel filter
4. changed oil
5. new battery and alternator.
6. Lucas injector cleaner (great performance improvement until the tank was empty)

then years later, I went back to working on the intermittent hesitation.
1. repaired small leak in exhaust near headers
2. small leak in intake (rigged up one high temp 2.75 inch diameter radiator tube to connect to 2" PVC (female) 45 degree elbow from home depot. smoothed out the insides with my dremel and a makeshift sander. used 2" black rubber sewer connections to connect the rest of the pieces together. DO NOT USE THE SEWER DIRECTLY TO THROTTLE BODY. WAY TOO HOT! I used them upstream by the MAF, and connection the tube above radiator. Do not lose the piece of insulation between tube and radiator.
3. ground cable on battery not tight
4. cleaned the spark plug wire connections really good and cleaned plugs
5. cleaned mud caked on the gas tank mechanism in front of tank, connected with some kind of metal cable.(cleaned with wd-40). wire brush.
6. throttle body gummed up with black stuff used o2 safe non-chlorinated.
7. Cleaned Mass Airflow Sensor with throttle body cleaner. and then with radio shack tuner cleaner...I hope this didn't hurt it.
8. adjusted idle screw
9. cleaned O2 sensor on CAT convertor
10. What I think it ended up being? A combination of the above, but! I noticed A stereo amp wire that someone ran along the body of the vehicle. It had a slight tear to it, which would explain why it happened worse on rainy days. The dampness could have completed an arcing circuit causing electrical power loss. If you do your own stereo installs make sure you fuse everything. and wrap it real good with tape or heat shrink flex tubing. I'm lazy and used cheap duct tape. I resealed everything with gorilla tape because I'm lazy again. this time I wrapped it with some electrical tape as well.

The truck runs just about perfect now. It peels off on take off if I want it to now. It hasn't rained in the past few days so we will see If it does it then. I'll keep you updated.
Thanks to this forum, I pretty much ruled out everything it could have been, and the truck got better performance at each step. All that stuff mentioned needed to be done anyway at 160,000 miles.

 

im having some sputtering on my 22re and rough idle...im thinkin its my 02. how did you clean your o2??