I'm struggling to find a problem with the stock pickups on any of my Fender Strats', some are the vintage staggered type and some are all flat, but they all sound great with no issues. I have to wonder if the strings are the main issue rather than the pickups.
Originally the early Strats had heavy stings with a wound third, possibly 13/56 gauge and I always remember the third string sounding weak on my '63 Strat. When I switched to lighter strings the problem wasn't there any more.
Recently I have been experimenting with different guitars and strings to obtain maximum comfort in playing, due to my hands being damaged by the chemo therapy I had and I can say that I have discovered my PRS SE Custom 24 is the most comfortable profile for me in my current situation. I have tried numerous different string gauges and settled on Ernie Ball 'Mighty Slinky' which are 8.5/40 with a plain third. Using the coil tap on the BareKnuckle Mule humbuckers which I fitted to the guitar I get a very good early Strat sound that is more than acceptable for my favourite Shadows tracks. This is something that I would have dismissed a few years ago, but my patience has led me to a very comfortable way of keeping up my musical activities.
I have a G&L S-500 with the pickups described by Pete and they are excellent and I would go as far as saying they are possibly the best Strat pickups that I own. They are nothing remarkable other than they have adjustable pole pieces (which I have never adjusted) but the sound is always excellent. I think Leo Fender's tone circuit on these guitars has a lot to do with the quality, the guitar is equipped with bass and treble controls that actually work.