On my friends 3rd gen (98) there is a rubber grommet that comes thru just above the brake pedal. Just cut a little slice in it and jam the wire thru then you can run it under the carpet to the door sill area or wherever you are going to.
Not a problem let me know if you have any other questions I had an amp in my old tacoma that is like your truck and put one in my 04 4-runner with 12" bazooka tube.
