The first and most basic thing you have to do is choose a guitar, based on looks, feel, and sustain.  The sustain can be improved, but not very much.  With the feel, choose mainly on the shape and with of the neck and the scale length and shape of the body. I suggest choosing a guitar that can be very versitile, such as a fender jaguar, or something.  Dont choose a really expencive Gibson or something, that you'll be scared to mod. Dont choose a guitar with humbuckers if you wanna put single coils in it; but you can choose a guitar with single coils if you wanna put in humbuckers.

      The second thing is choose your pickups.  Choose the sound you like, and get those pickups.  If you play a lot of metal and stuff, choose some hot pickups with rails or something. If you wanna put humbuckers in a single coil space, get stacked single coils, or get someone to carve out a cavity for them.

       You may want to change the pots and capacitors. This can brighten your sound. Helping you get different tones. (buy the capacitors at radio shack, there rly cheap)

       There are a few things you can do to change the feel of your neck. You can always make it easier to play by scalloping the neck, but before you do this, you should try playing a guitar with a scalloped neck.  You can also make it easier to play by putting in larger frets.

       There are a few things you can do to increase the sustain, and they do work, but only to an extent. Im warning you, if your guitar doesnt have sustain this wont give it tons of sustain, it will just give it an extra push.  If you have a tremolo system, you can replace it with a stop tail bridge, or just put washers under the part that goes down, forcing it to be in an upward position all of the time. You can also attach a graphite nut and tree.

         Some other things that you can do is install a bigsby vibrato to a solid body, put in locking tuners, put in a phase switch, put in a switch to make the pickups wired in series.

Things i dont think you should do:

DONT REFINISH YOUR GUITAR

DONT "RELIC" YOUR GUITAR
DONT TRY TO MAKE YOUR OWN PICKUPS (unless you know how)