well its your guitar so anything you want you can to do it! as for inlays they can be tricky, just take your time on everything and remember to measure twice and cut once, it save you massive headaches in the end! also i will give you a rundown of the guitars i am building right now just to give you an idea of what you might want to do.
im building 3 randy rhoads V's right now and they all have the same specs,
25 1/2" 24 fret maple neck thru body (self explanitory the body is glued on the neck forming the guitar)
ebony fret board (sharkfin inlays on 1, scythes on 1 and reverse sharkfins on the other)
body woods (or wings as there sometimes called) alder on two of them and mohagany on the other
1 5/8" nut
floyd rose trems (1 black, 1 chrome, 1 gold)
all of them will have dimarzio x2n's with neal moser 10x booster switches and a vol knob.
recessed straplocks and strat jack on the back of the guitars
im also building a neck thru jem, warlock, ironbird and drawing out the temps for my stealth too
thats another thing, making templates now for everything you need will save you a lot of time as well if you plan on making more guitars (like most of us) i have quite a few templates for bodies, pickups, cavities etc, making templates takes sometime because you have to be precise but it pays off BIG TIME after your done with your guitar.