The best choices when designing a guitar are often those that allow the most versatility.
My advice on the subjects mentioned
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Neck: Whatever shape you find comfortable in whatever material you like the sound of. I've heard that thicker necks have better tone, but to be honest my own ears have never been able to convince me of this. If there really any such difference it has to be so subtle you would have to A/B hundreds of guitars to identify it.
Fret wire: Buy high quality. You want to buy fret wire that you know is hard and will last. I think that it's better to install fret wire that is too tall than too short.
Body: Whatever you like that isn't too heavy.
Pickups:
Bare Knuckle hand wound pickups.
Strings: Whatever you find comfortable. There isn't any advantage to using strings that sound great but murder your fingers.
"If one has realized a truth, that truth is valueless so long as there is lacking the indomitable will to turn this realization into action!"
-A.H.