Pickups to taste will be the biggest change. I will replace pots if I don't like the taper or because they don't last, and when doing so, if not before, I replace tone caps with basic but good foil types. Hard no to snake oil or ceramics. I also almost always replace the selector switches because as simple of a deign as they are, for some reason the cheap copies don't last reliably. Input jacks I usually keep until I have a problem which is rare.
Like pickups, 50's vs 60's wiring is a matter of preference. Same goes for things like split hum buckers and series/parallel switching. I have tried it all, and I have come to the conclusion that if I like it as a hum bucker, I will probably not like it split, and I gravitate more and more towards simple switching as I find myself not using the options anywhere near as much as I think I might.