The 500k are supposed to give a brighter sound are they not? I think it'd be down to personal preference really. My guitar used to have 3 single-coil pickups in it, but still used 500k pots. Odd The pickups were crap so the sound wasnt all that good. Now i have H/S/S, but i have rail type single coil sized humbuckers, so i really have H/H/H configuration. I use 500k volume and 500k tone, sounds maybe abit too bright. Maybe i shouldve used a 250k pot somewhere, or maybe i need as bit more bass in my sound.
Im sure you can do what you originally thought...i have schematics back at home i can check later.
edit: I found it (3rd pic down on the left)
I dont think there will be any benefit from using 50v caps....you can use a really high value cap to protect yourself from faulty valve amps (and that connected between signal ground and actual jack-ground) but as far as normalguitar wiring, the current and volatge is quite low
I think people leave about 1/4" or if using a figured top or want more than 1/4" thickness, longer shaft pots are used.