sounds cool, i always wanted to do this. only thing i would say is if you already have a strat ( this is an assumption when you said fender) what is the point of making a guitar that is exactly like a strat, sure take inspiration from it but dont copy everythin. so if you want to use mahogony go for it, it mite give interestin results. on the other hand ther might be very good reasons fender doesnt use mahogony so please reasearch it before jumping to conclusions.

as to other stuff i would put a humbucker in the bridge position and then get coil taping, or the ability to switch the humbucker from series to parralel. this would give you humbucker and single coil sounds.

also you might want to look into gettin a whammy bar with piezo pickup in it. if you didnt know these give quite good acoustic tones. well at leat i think they are cool especially when you can blend them with the normall pickups. this might not be for you but i would do it. if you had loads of money to spair ( this isnt really that serious) you could buy a line 6 variax, remove the whammy bar/ piezo pickup and all the electronics, and put it in your custom guitar. then you would have a large arsenal of tones. but this is a bit over the top money wise.

things you should also consider are what scale length of neck you want, the fret radius and the profile. but if your used to playing strats you might as well stick with the standard strat neck.

as i said it sounds cool. keep us posted with progress and show some pictures, plz.