The pickups matter for squat; just use a decent set, Fender Custom Shop SRVs/Fat 50s, Rio Grandes, Fralins, whatever; as at the time he was playing a '70 black Strat with a '57 maple neck, a set of Fender Custom Shop '69s would probably be the closest thing to the original you would pick up without spending thousands needlessly for vintage gear.
I will reiterate, the pickups, as long as a decent set are used, mean NOTHING!!!! Go Google on his gear, he has a smorgasboard of pedals, some custom made, TWO effects rack and at least one effects technician. Much has been made about his EMG endorsement, if you have his new live DVD he plays it on a couple of songs, doesn't really sound a lot different that the black axe with whatever PUs are in it now. The kid playing guitar touring with Roger Waters nails the sound dead on (see Live 8???) playing what appears to be a vintage Telecaster.
It's mainly about TECHNIQUE.
You can approximate the sound if you play in that style with Strat -> Wah -> Overdrive (setting varies) -> Chorus -> Delay (varies) -> Flange (on occasion) -> Distortion (sometimes) -> tube amp; not necessarily in that order.... But you have to have the playing technique.... If you can't play blues seriously you'll never get Gilmour