The OEM JBL system in the 4runner is crossed over on the amplifier and cannot be modified (crossover points nor gains). Not sure of the exact crossover point, but somewhere around 300 (+-100) Hz for the front speakers. The front doors play the lower frequencies and the dash the highs. The speakers that you listed have very different sensitivity values with the 3.5" at 83db 1w/1m and the 6x9 at 93db 1w/1m. So the doors will sound quite a bit louder relative to the dash and the fader will not do much as they share the front channel. I would look for speakers that have similar sensitivity for the front doors and dash so that they are level matched and sound at the same relative volume.