PUPs are the most overhyped, overblown and overrated mod you can make. I swap them out all the time (LOL), but really by the time you amplify and add effects, and play at stage volume, they just don't matter a whole helluva lot. And they are strictly personal taste, and HIGHLY subjective. Spend your time and energy on the playability (and reliability) of the guitar.
1. You'd do better to save your money on the PUPs and drop it into Tuning Machines, fret dressing file, a couple pots, a switch and a soldering iron. You'll end up with a rock solid, reliable instrument. I've replaced about a dozen trems/bridges now. I've come to the conclusion that this matters about as much as the PUPs. Personal preference, HIGHLY subjective. Dress the sharp edges of the frets (fret sprout) on the neck edges. Take the shaft of a screwdriver, and run it along the neck edge (between the frets...also called "rolling the fretboard"). The 35$ set of locking tuners from azguitarparts.com are pretty nice. Also, don't be afraid of unscrewing the neck and adding a shim (if it's a bolt-on). Try a business card, or credit card strip at the front of the neck pocket, if your action is too high. It's super easy, and the best way to understand what shimming does is to try it. It's easy and free.
2. If wanna take it to the next level drop $30 a fret leveling block and some 220 grit sandpaper and a crowning file ($45 on stew mac). You'll end up with playability at as low (or high) an action as you wish.
Great tutorial on fret leveling from TDPRI
3. If you wanna get to the point where you can take a $100 SX or $100 partscaster, and make it play as well as
any of the biggies, drop some coin on nut files, and nut blanks. Learn to cut a few nuts. Nut material doesn't matter. This is another case of cork-sniffing, overhyped, ********. For tone, the nut only makes a difference on open strings, and I challenge anyone to tell the difference between bone, micarta or plastic in a blind test. I use micarta because it's cheap and easy to work with. The most important part of the nut is how the strings lay in it, and how it affects them returning to pitch after a bend or trem dive.
Great Tutorial on making nuts from TDPRI
Do this on a few cheap, or beater guitars. You'll quickly find that you can make some gems out of Craig's List or Yard Sale bargains. They won't be worth much as far as resale goes, but they'll play awesome. I sold a partscaster to a guy 2 weeks ago, he played it for 5 minutes and said he had to have it, that it was the best playing guitar he'd tried in a long time. Guy handed over my asking price, no haggling.
I sold Eric's old SX Tele too, same deal. Guy couldn't believe how well it felt and played. This was a bastardized guitar, with no pickguard, a Gibson P100 (P90 with a dummy coil, universally reviled on online reviews) and a cheap-*** bladed humbucker with ceramic magnets in the bridge. Once I demoed the dead-nuts, Keith Richards Satisfaction tone from the bridge and he played it for a few minutes, he reached into his pocket and gave me my asking price.
I don't polish the frets (playing it will do the same thing) to take out the crowning marks. I slip with the dressing file and leave marks on the neck. I don't polish the nuts, I lose the trem covers. I use rusty screws for the PG. I plug stripped pg holes with toothpicks and glue. None of this stuff matters...The point I'm trying to make is just grab a cheap guitar and get to work. I level fretboards while I watch the Browns and Indians lose. Just stick the neck on the carpet and start grinding. You don't need anything elaborate if you don't go OCD or anal about perfection.