The center speaker presents a few problems:
1 An excessive amount of sound fron 5khz to about 16khz
2 The signal from the center speaker is a simply summed signal. The wires from both the left and right channels are both connected to the speaker terminals, destroying much of thestereo imaging. Kind of a poor man's Dolby Pro Logic...
3 With frequencies in this range it is oftem beneficial to deaden reflections within the first 1ms or so (primary reflection points). In home theaters we often try to minimise primary reflections. Toyota unwittingly provided a primary reflection point (windshield) within inches of the driver. This contributes to a perceived "harsh sound".
The elimination of the sound from the center speaker helps with all of the above issues, but leaves the frequency response still off a bit. The resultant frequency response is down slightly at 16khz which can be helped with a click or two of trebble added in the sound controls. Otherwise, it's a pretty good curve (not flat, more of an inverted bell curve as it should be)
The effect of eliminating the center channel has the effect of increasing the subwoofer sound level with respect to the original overall sound.
I did this and was initially unsure if I liked the effect. The imediacy of the sound was reduced, and volume levels had to be increased to make up for the change. After a week, I reconnected the center channel and was repulsed with the resultant sound, so it's disabled for good.
The sound of the stock sub is much better with the higher required overall volume level (# on the Head Unit) with respect to stock.
On another note, I think the amplified signal to the sub is rolled off (~30hz?), but I have to measure it to be sure.
If you want to try disconnecting it, it's reversible. Follow Castaluci's (sp?) directions for removing the stock head unit, but don't actually remove the head unit. Instead, look for the speaker connector above the HU on tword the left. Disconnect and see what you think.
BTW, my settings are fader centered and 1 click of extra treble on the 07 NAV... Should be similar to any JBL on the 4Runner.
Sean