Since you're designing a neck-thru-body guitar, I recommend using maple. You could laminate a slab of mahogany on top (a la Les Paul), if you think it might be too bright, but since I found an old all-maple, neck-thru-body Odyssey V, I have come to question that assumption. I find that the thick, dark sound associated with mahogany is as close as the Tone knob. And I can still get as sharp and trebly as the pickups will allow.