SSL-1's if you want it to sound more like Rory did years ago...by now the pups in the strat are more mellow...Antiquity Surfers if you want it more mellow...word of advise, don't go with a "hotter" bridge pickup.
You also probably need a treble booster - if I remember correctly, the crispy cream (krispy kreme??) is a fair reproducer of the old Dallas rangemester tones (there are others, but I have no experience of them)
Rory used a set of stock strat pups, in 1961 the bridge pup would have matched the neck as well as the middle. The whole idea of a hotter bridge pickup is a more modern idea, I mean you could use one, but Rory didn't.
I think the pickups from Rory's old Strat were rewound at some point when he had problems with them.
In this interview he mentions some other pickups, but......
"With the Strat, I changed the lead pick-up for one of Fender’s hot x100 jobs, and I’ve tried the Fat Strat pick-up as well, but I always come back to the original."
Cool info Simon thanks. I love his playing and tone. He is definitely one of the best players/writers ever.
That said I think a set of surfers is a close as you can get to his tone. Van Zandt blues bridge, and vintage + neck and middle almost nail that tone as well.
You should use the bridge+middle position with the middle tone rolled off, if you like Rory's sound. Try that into a cranked Fender Bassman and you might be surprised!
He had a live version of "Messin' with the Kid" that just was jaw dropping. If you went with an Antiquity or Vintage, you'll catch the essence of his tone.