Check and see if your main intake tube from the mass air flow sensor (MAFS) to the throttle body, is cracked or is loose on either end, I have seen Toyota's run fine at idle with the a leaky intake tube, but as soon as there is drag put on the engine they will sputter and sometimes quit. The fuel filter is are very easy to locate on the 3VZ-E 4Runner, it is on the passenger side frame rail by the transfer case cross member if you want to replace it, I would. You can also unbolt the fuel tank skid plate, and take out the drain plug on the tank, to get all of the water and junk out of the tank. Finally if you want to try it, you could pull your air cleaner out and while it is idling you can reach up inside the mass air flow sensor and move the flap in a little while you open up the throttle, see if you can get it to rev up better by overriding the MAFS, if you can get it to run better then it probably has a vacuum leak somewhere. To find it you can spray a little WD-40 on the lines and if it all of a sudden revs up then you found your leak. Good Luck hope this helps.