ahh Nick you're better researched than me. On his recent solo tour he is definitely using more vintage pickups in a black strat. i assumed they were vintage fenders (and thought i heard the same info) but could be dimarzio's. However my understanding was that his main red 57 strat is still loaded with EMG's - Gilmour signature model. At any rate, on his live solo dvd you can definitely hear the difference between that and the EMGs from the 80's.
Heh, I'm a Gilmour nut...
The black stratocaster you're referring to is actually known as (quite aptly named) The Black Strat (yeah, real original...). It's a '70 Strat that's been heavily modified over the years: it's got a Fender '83 Reissue '57 Neck, a black pickguard, a Callaham shortened trem arm, and a switch that will mix in the neck pickup with the bridge or middle. In the '80s, it also had a Kahler in the '80s, but it has since been removed; you can see behind the trem, there's wood that filled in where the Kahler previously was, and it's been painted black. This is the strat that the Fender custom shop recreated, if anything this could be considered the Gilmour "custom" strat. He did have his own EMG set, which has since been removed.
If you want the scoop on Gilmour's gear, gilmourish.com is great.