I don't think I have a guitar that's stock (my Martin acoustic is stock, but not my electrics). I look for something that suits me well overall then tweak it a bit to my liking. The fewer tweaks the better- sometimes just a small wiring change (like so called '50s wiring). Sometimes its a matter of improving quality, usually of electronic components.
To be honest, as much gear as I have, I don't have much to mod anymore. I only have one piece of Fender gear- my '66 Vibrolux Reverb and one Gibson (unless you count my '64 Epiphone Olympic and recent ES-335 Pro). The Gibson is my '59 ES-225TD.
My Tele, Strat, Princeton Reverb, tweed Champ and Deluxe are all really nice clones, mostly built by me and tweaked to my liking. Although you might consider them to be pretty extreme mods, they're pretty close to the originals. Other than the ES-225, my Gibsons have been replaced by Carvins.
I just do what works best for me (that does not include refinishing guitars).