I wired an HSS configuration like I found on Seymour Duncan and am not liking the sound i get on position 4 (mid + bridge). I went to Fender and found their diagram for Mex Fat Strat.

http://www.fender.com/support/diagrams/pdf_temp1/stratocaster/0134700_02C/SD0134700_02CPg2.pdf

I must be missing something as I can not see where the red wire goes on a 4 conductor wire humbucker. Also, I would like to have tone control for the bridge pickup; as I was able to do so with the SD diagram. Any help out there?

Premising you are using a Duncan HB, here's the wiring correlation, based on the Fat Strat (FS) diagram:

The red and white wires of your Duncan are the black and white wires on the FS diagram; the black wire on your Duncan is the green wire on the FS diagram; the green wire on your Duncan is the ground wire on the FS diagram.

Naturally, the bare wire on the Duncan is a ground wire too.

IF you find that once wired, the Duncan is out of phase with the middle pickup, reverse the Duncan black and green wires.

As to the tone pot for the bridge pickup, all you have to do is move the white wire from what is currently the middle pickup's tone pot from the middle pickup's terminal on the toggle to the bridge pickup's terminal on the toggle. Be advised though, that your middle pickup will no longer have a tone pot and due to the auto tap wiring, you cannot use this tone pot for middle AND bridge, it has to be one or the other. Unless of course, you want to lose the tone pot for the neck pickup.

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You dig?