1) Buy good quality parts. Even kits can have rubbish in them. The best thing to do is ask a guitar tech for what he recommends.
2) Use innovative wiring. My diagram below is based on Craig Anderson's idea on volume pots:
The extra capacitor means as you turn the volume down, more treble passes through, so you get good rhythm even when the volume is low, neat mod!
The rest of the gear are just good values to use, but 250k pots and 0.022uF capacitor on the tone can be used (as the Seymour Duncan website suggests).
3) don't scrimp on the wire. Get good solid core wire with a low resistivity. Good solid soldering also helps, that's the contact after all.