my sons 4 runner with the 3.0 has been sitting for 3 yrs but we start it now and then .recently it started running very poorly and then would not run at all.we traced it back to the fuel pump and replaced it .
the old one was very bad,rusted and definitely quit.in that time the battery took a crap too and would not come back with the charger so we replaced that too.once we started it again it ran great
and seemed fine.we let it run for a half hr or so.now every time we start it it runs very poorly and we have to keep playing with the gas pedal to keep it going but after about 5 min something seems to click and it immediately
starts running smooth again.the tank was nearly empty and ive been filling it with high test 3 gal at a time.there was no water in the tank when we changed the fuel pump.any ideas as to why its running so badly as we srt it up now?

 

Have you changed the fuel filter thats under the frame on the passenger side? It could be clogged and stopping flow.

If that is okay I would move on to making sure the lines themselves before and after the filter aren't clogged. It sounds like if it runs okay for a bit but then struggles it is having a hard time getting fuel still. If I were you I would test you're getting good flow by undoing the hose clamp to the soft line that's the fuel return to the tank to check that you're getting flow when the key is in on but without starting the motor.