Dear Kyle: I'm responding to your post because I feel I may have some meaningful feedback (but judge this for yourself) insofar as I'm the proud owner of one of Alembics' most elaborate customs to date, and it has many similar elements to your specifications. My custom 8 string bocate Europa bass can be seen in the archives (C.o.T.M, June 1999), and also my recent allow me to formally introduce myself thread (in introductions). It has a flame maple body, as well as a 13 piece neck made of ebony, purpleheart, rock maple, and flame maple.
First of all, though you're a youngster, you seem to have a fairly clear idea of what you want. This is good. Yet, you're seeking feedback. This is also good. I'll give you some.
First, let me ask you, are you dead set on the Skylark body and electronics? I strongly recommend you familiarize yourself (assuming you haven't) with the Q function on other Alembic instruments. I consider it an indispensible tone-shaping tool, and cannot conceive of an Alembic without it; I think if you had the opportunity to play an Alembic instrument with a Q switch/function, you might well also insist upon it. The versatility it adds to the Alembic low-pass filter cannot be adequately described with words. In my opionion, anyone who has the filter without the Q switch is missing out, and only getting half the picture.
With that said, I'll echo what Tom Z said. Mica has said that Alembic's experience indicates -WITH NECK-THRUS- that the choice of neckwoods and the electronics package are the main factors that influence the instruments sound; body-wood is next, and top/back laminates are last.
Rock maple is the traditional neck material; it is strong and consistent, and has a bright sound. Purpleheart is denser, and increases sustain. Ebony is denser yet, and increases sustain more. Adding a combination of these will increase sustain... but also the mass/weight.
Flame maple is less dense than rock maple, and has a warmer sound, more like mahagoney. Because it is less dense, it is also less strong. At the time of my commission, Mica told me they wouldn't generally recommend it for a neck material on a bass. Of course, a guitar has a shorter scale with less tension, so it is less of an issue (on my bass, the flame maple laminates are the outer laminates of the neck, and therefore less relevant structurally, as well). So if you had a 5 piece neck with flame maple laminates on the outside, it would surely be fine. You might consider having 2 ebony laminates and 1 purpleheart instead of your configuration -though it'll surely look and sound good either way... but ebony is even more awesome than purpleheart.
Maple typically has a bright sound; flame maple is a little warmer (as opposed to bright).
The concept you have would likely produce a guitar with a warm/bright sound with substantially above average sustain -as well as above average mass/weight. (Although I wouldn't say it would be anything to be afraid of).
I'd definitely recommend (again) familiarizing yourself with the Q switch on Alembic instruments... without it, the low-pass filter only has half the magic. Also, you MIGHT (or might not) want to consider the quick change tone changed switches on the Europa/Rogue basses. These are 3 position toggles that can boost or cut the treble and bass +/- 6 db. They are very handy. Of course, they could give you full rotery knobs. But this seems less important on a guitar, for some reason. (I play both bass and guitar).
Another issue is whether or not you want mono or stereo electronics. Again, it seems less essential for guitar to have individual tone control for each pickup, but it is an option that Alembic could deliver, if you wanted it. I actually can't recall seeing an Alembic stereo guitar, although I'm sure they've made 'em, and I've either forgotton or just never seen 'em. But they could do it, if you wanted.
Check out the electronic packages on the Signiture series, and on the Europa/Rogue basses.
I'd recommend having the Signature electronics with added (bass + treble) boost/cut switches for each pickup... it would give you mind-blowing versatility... in lieu of this, I'd recommend the standard Europa/Rogue electronics for your guitar, which would give you essentially the same versatility, except in mono instead of stereo...
Good luck with your project, Kyle! I look forward to seeing it. By the way, the choice of colors... the vermillion accents... is great!
One other thing you may (or may not) be interested in is the bookmatch to center option for your front and/or rear laminates. Just something to think about.