NO help with the BKP but know some on JP.
He does use DiMarzios.
It is a Air Norton I think and a proprietary one of his design.
As for the acoustic stuff, his guitar is equiped with piezo. He can mix the piezo with the pups or use just magnetic pups or piezo.
He runs a stereo setup into an AD box.
He has a HUGE effects/backstage setup. But thats about what he does.
This is a pretty cool lil film of him showing some of his stuff.
http://www.youtube.com/watch?v=e2uklZ7_C5s&search=john%20petrucciCourse he also uses Mesa, Lonestar and Roadking I think.
I have ordered a JP6 myself and tried one this weekend. But was through a Marshall so not exactly JP sounding, although it did sound good.
Bear in mind his pickups are also NOT adjustable. They are afixed directly to the guitar body and he has a fair bit of air between the strings and pups for his preference/style.