Re: I have a strat with an SSL-3 and Fender neck, middle, so the Polarities don't mat
95% of the cool sound of singles is just that...the single coil sound. With noiseless/stacked etc pickups you lose that subtle "breath" and "sparkle" of a true single. IN the end you have to choose between living with the hum, or living without the subtleties.
If you play with a lot of gain, then noiseless are useful, but if you don't then for a slight decrease in hum its not worth losing the sparkle.
Re; polarity. Its not a big deal. Personally i prefer it when the middle pickup is not rw/rp to the other two. Position 2 and 4 wont hum cancel of course but the old skool non-cancelling sound is fatter and more organic for me.
Getting the perfect strat set up is very much a personal preference and the result of trial and error tho, so go for it and let us know what you find out.