It's hard to tell if a pup upgrade is a good idea without trying the guitar. Now I've never played Pacifica but heard some good reviews, and if you still love it after 8 years I bet it must be a more than decent guitar.
What I can say for sure is that, on the two guitars I upgraded with BKPs - a MiJ '81 Vox Custom 24 and a CiJ '62 RI Tele custom - it made a huge difference, and was definitly worth each and any penny.
wrt/ your own guitar, and from the styles and player you mention (BTW, yes, Frusciante, Hendrix and Gilmour are mostly strat users), I'd suggest Mother Milk or the new '62 spec'd (not officialy released so far) - or eventually Irish Tour for more midrange OD tones - strat single coils, and a Crawler bridge. Now I've never tried the BKP strat sets so far but I think you're mostly after these early 60's specs (Hendrix, Frusciante...). I do have a Crawler set on my Vox Custom 24 and the bridge pup is just great for blues to classic rock to old school hard rock to hardcore punk - lots of bite, sharp as a knife yet still warm, singing and never harsh -, and it's been designed to work well on brighter woods (alder, maple etc).
FWIW, we seem to have similar tastes, and the above set(s) are what I'd personnally put on a HSS strat 8)
My 2 cents...