I like the way the mid/neck sounds. the bridge is useless, imo. I would kind of like to replace all 3. i love SRV's tone, John Mayer's tone, etc. That fat, essence of strat strattiness that also overdrives really well and distorts nicely.

Which pickups should i go for? I've heard fender custom shop 54's recommended, as well as Kleins, CS 69's, and lindy fralins. I've listened to some clips on line but is that really a great indicator? With installation it's going to be $200 at least, so i'm just asking you guys for some input. Also, how much of a diff will be noticed in quality between what i've already got? The strat is a 2013, so it have "fat 50's" pickups.
The Fender Big Dippers are absolutely phenomenal for gaining that sound. Lots of quack without being too punch in the mix, great underneath growl. I love them.

The only problem is that they only come on the John Mayer Signature Strat, so you'll have to find them on eBay somewhere. A close second would be the good ol' Texas Specials.
I've heard good things about the custom shop 69's, bareknuckle mother's milk and lindy fralin's. it's just a lot of $ to spend on the strength of online clips.