Welcome to the adventure! Sounds like you have an idea or two about what you're after, but mayhap you could embroider a bit...
Are you looking for a plain clear finish on that body? Rosewood top on mahogany suggests "yes," but please confirm.
In any case, do you plan to finish it yourself? There's lots of wisdom on this board that will help you get where you want to go, but know this going in: The road to a good DIY finish is fraught with tedium. Shortcuts abound, and all of them lead to folly. If you aim to finish it yourself, plan on making lots of time to do it right. Doing it wrong can take forever, too, but you can get it wrong a lot faster than you can get it right. In short: Practice on scrap, make your mistakes on cheap wood, and be patient.
Electronics-wise, I am nobody's idea of a guru, but we do have a few around here from whom I have learned the following:
Complexity for its own sake can be gratifying, but simplicity is generally more useful for the gigging musician. What you describe below is cool, as far as it goes. Three decidedly different flavors of humbucking pickup = mucho boss tones, presumably. But the three-different-tone-knobs thing sounds like a good way to drive yourself nuts. There are those (see, e.g., one of our resident pseudo-lunatic genuine-philosophers, StubHead) who makes a very good case for the Les Paul-style two-vol-two-tone configuration; but three tone knobs (and their tendency to monkey with one another's performance through unexpected interactions) could be really difficult to rapidly get useful sounds out of when you're up there in the heat of battle.
All I'm sayin' is, if this is your first go-around, maybe a single volume and a single tone knob will get you where you need to go, and you can do some studyin' and learnin' to determine whether the more advanced electronics are really where it's at for you. Start simple. Go slow before you go fast. You can always drill more holes and string more wire, but plugging holes is a pain.
That said - if you have your heart set on it, or if you are more experienced in wiring than your initial post discloses, go nuts and tell us what you learn on the way - because I, for one, have learned a lot from others' experiences on this board, and others would likely appreciate the benefit of your voyage through soldering hell as well.
For the neck:
Good call on the stainless frets. They're slick and nifty and so-forth.
Lumber-wise, I'm a big fan - and many others here are as well - of the no-finish-required tropical hardwoods. My personal favorite is canary, but many here swear by the tactile joy the silky smoothness of pau ferro provides. Canary is reputed to have maple-esque sonic characteristics, so if you'd like to replicate what you already know, soundwise, that may get you there. PF is rumored to be "darker," which I take to mean it rolls off some of the higher-frequency snap associated with maple necks. Rosewood, of course, would echo your choice for the body's top, and if you order the neck and body at the same time you could encourage the builders to match the color and grain, which would be triple-x sexxxy. Like PF, rosewood is reputed to be "darker" than maple, which will vary per specimen, but is likely to be generally true. There are a lot of Musicman axes offered with rosewood necks these days, and you can try a few out if you live near a Guitar Center. I like 'em.
That said - nobody ever got fired for buying IBM, and you can't really screw it up too bad by going with maple. If you should decide to go with maple or canary, I'd suggest an ebony board, or if you can spot one, a rosewood board to match the body top. My opinion is that the fingerboard does little to alter your tone, but a deep black fingerboard always looks like class.
You don't mention it, but here are other things to consider:
1. What bridge system are you using? If you're going with the Jazzmaster-style bridge and twangbar, the Mastery part is deemed by some around here to be decidedly superior to the Fender although a bit pricey. But hey - you're buying Lollars, so what's a few more shekels among friends, right?
http://www.masterybridge.com/
2. Locking tuners. Forever and ever, amen.
3. Pot and capacitor values are worth considering. Vintage-style caps are snake oil. High quality pots are not. For your mostly-humbucking mahogany-bodied guitar, 500k pots and 22pF (also expressed as .022 µF) tone caps will probably help keep the top-end edge you want, especially if you go with a "dark" neck wood. The pots Warmoth sells are not my first choice. I've destroyed a couple pushing the knobs on and driving the shafts out of the open bottom. Get closed-bottom pots. I have gotten CTS pots and lots of other doodads from Guitar Parts Resource and been very happy with price and service. http://guitarpartsresource.com/
4. Washers with soldering lugs are easier than soldering to the bottom of the pot. http://www.guitarpartsresource.com/electrical_shield.htm
Final observations:
If you get into it and you find yourself getting pissed off when something goes sideways, step away and do something else. Angrily forcing your way through an error or unexpected slip is a good way to make it worse. This is supposed to be fun, right?
Best of luck, and keep comin' back.
Bagman
