Those SE pickups aren't that bad actually. If you really wanted something "better", my go-to for that kind of stuff would either be Seymour Duncan '59's or DiMarzio 36th anniversary pickups. If you want something hotter than vintage, than the Seymour Duncan Distortion is really good too.
in the neck this true, but not the bridge. Basically, the 59 has more bass in the neck and under too much distortion you get a "woman tone" which can be cool if you want that, but if you don't want it you might be stuck with it [or have to back down the gain]. The 59 set is great for blues and classic rock stuff. changing in the jazz neck is a great idea for higher gain. The JB in the bridge is quite a bit hotter, so getting low gain tones can be a little harder because the pup is naturally so hot. Personally I prefer the distortion to the JB in the "hot" arena.
I have a set of SD 59's in my PRS SE Singlecut Korina. (The set is called Vintage Blues). I mainly play blues/classic rock, and don't really use a lot of effects, and not a lot of gain. I love clean tones, with a little grit, and the 59's do that very well.