I have a 1998 4Runner too. Every 10000 miles I would drain the transmission fluid at the bottom (only taking out part of the total ) and put in new fluid. I think it was about 4 quarts. Worked great for me, as i have 250000 on this transmission. I put the new fluid in the dip stick for the transmission and off I go.
On my 2004 there is no dip stick. How does one put the fluid back in?
The new fluid gets put in thru a fill hole on the side of the trans just ahead of the transfr case. The pan has 2 plugs on it, one to drain and one to check the level (says "check" on it). The level has to be set at 96-108F.