In my opinion the tuner config would not make one jot of difference. 3 by 3 or 6 a side, its just the design aesthetics that count, what looks best on your guitar.
Maple neck vs Mahogany: traditional wisdom says more top end with the maple, but a good hoggny body will still give you plenty of deep warm brown tone. The top end should be further accented by going for a bolt-on rather than set. result: the perfect hybrid between a les paul, a strat and a prs.
I made up a single cut guitar recently, HB's with coil tap, mahgany body, thin maple cap, bolt on maple neck, it has loads of bottom end but a really nice clear high end that cuts through, really good balanced tone, for me, tonally, its near-perfect, just a little shabby on the finishing off.