My number 1 guitar is an American Deluxe SSS Strat which I absolutely love. My main tone is the #2 pickup position(bridge/middle). It has the bite of the bridge pickup, yet retaining a bit of warmth from the middle. It's perfect for low gain tones and cleaning up with the volume knob. The S-1 switch allows this pickup combo in series, which is a tad hotter and thicker. I'm not in love with the humbuckerish sound of the bridge/middle in series(S-1), and would much rather have a real humbucker in the bridge. The harmonics just aren't the same as a real full sized humber, close but not quite.
I don't really care much for the S-1 tones(pickup combos in series, and all 3 at once in parallel). They are ok, but a real humbucker would be better.

Here's my thoughts:
I totally love the bridge/middle in parallel tone.
I want bridge/neck in parallel like a tele.
I want full-sized humbucker
I want to be able to coil-tap the humbucker, combined with the middle pickup, and get close to the tone I've been getting with my SSS bridge/middle.
My query is this: Can I get all these things?
I'd like to have a SSS guitar and a humbucker guitar like a PRS or Les Paul or HSS Strat, but I can't afford another guitar right now. And I know I won't be happy with a low-end guitar, so I'll wait until I can afford to buy exactly what I want. If I can make this work, I'll have the perfect guitar(for me). It'll be capable of all the tones I want. I'll be able to play everything from country/tele chickin' pickin', blues, classic rock and pop rock, and gained up stuff like Andy Timmons.

_________________
2010 American Deluxe Strat Sunset Metallic - Lindy Fralin Blues Specials in the neck and middle, Dimarzio AT-1 humbucker in the bridge.
PRS Custom 22 with solid rosewood neck
Mesa/Boogie Electra Dyne 1x12 combo
DRRI

All are doable. The only question is, do you want to work with only the OEM electronic components in the guitar or are you willing to add and/or substitute some? See, if you work with only the OEM stuff, part of the rewiring will cause you to sacrifice certain OEM functions here and there to achieve your requirements. You've already mentioned two OEM functions of which, you have no use for so this may not be a problem. Now if you choose to add or substitute components, specifically, adding two mini-switches or, substituting two push/pull pots or two more S-1 switches for your 'regular' tone pots, you can have all the combinations you have now (whether you ever choose to use them or not) plus your additional requirements.

Also for your consideration: You want to coil tap the full sized HB so that it can sound like a single coil (SC) when combined with the middle pickup. As you know, a SC is not humbucking. Consider wiring the full sized HB for series/parallel functions. This way, when switched to parallel, the full sized HB will surely emulate the SC tonality yet it will still remain humbucking.

_________________
You dig?