For an HSH set up, I'd suggest a Carvin Bolt Plus kit. You won't find it on their web site, only the regular Bolt kit, but if you call them and ask for Sean or Charles, they'll set you up. Every option that is available for the factory guitar is available for a kit, so, for body woods, if you don't want the stock Alder, you could choose:
Swamp Ash
Mahogany
Walnut
Koa
Maple
and you could also mix woods like a Mahogany body w/a Maple cap. You could even vary the Maple cap by just getting Maple, 'figured' Maple, AAA Flame Maple, or AAA Quilt Maple. Or you could put a Flame Koa top on a Swamp Ash body; all kinds of options. For necks, you could get the standard Maple neck w/an Ebony fingerboard, or get a Birdseye Maple fingerboard, or Rosewood. You could get a neck from:
Mahogany
Alder
Koa
Walnut
and you could do various laminations of those woods like a 5 piece Maple/Koa/Maple/Koa/Maple, etc..
On that neck, you'll have a choice of about 5 or 6 different fret sizes including a stainless steel fret option. You can go w/the standard pearl dot inlays, or abalone, or no inlays, or pearl block, or abalone block.
You have 2 different kinds of tuning keys to choose from (I'd get the Sperzels), 3 or 4 different bridges, several wiring schemes/switches/pots, and I think 11 pickups to choose from. 3 colors of hardware and straplocks if you want them. They'll even finish the body and neck for you if you want from a solid color to a 3 color step stained burst.
Go w/a stock set up and you're probably at around $450 or so and doing the finishing of the body and tung oiling the neck yourself. Option it to the hilt and have them finish it w/the most expensive finish and you're probably around $900. I'm guessing. When you're done, you'll have one of the best playing guitars you'll ever own. Here's my Bolt-T kit: