Congrats! Just got my first PRS this week, a S2 594 SC. I agree regarding the sustain, those .010's just ring forever.
I wasn't super happy with the pups initially either but lighter strings helped somewhat with the muddiness. I'll see how well I can tweak my FM9 modeler settings over the next few weeks. When you switched yours out did you change the pots or any of the other electronics?