Hi,
1) PBP3 will install as its own entity, in a separate folder, with its own set of device specific .inc files, completely isolated from any other versions so you can safely have both. I've got 2.6 and 3.0 installed and have been switching between them. I don't use MPLAB as my IDE though so I don't know about having both "plugged in".
2) It should. However, if you're setting the CONFIG-bits from within your code (as opposed to relying on the deafults in .inc files) PBP3 changes the way the CONFIG-bits are handled - to the better. I think that the old way is still supported but don't take my word for it. When you install PBP3 you'll get the manual as .pdf, open it up and check the #CONFIG/#ENDCONFIG directives.
3) Personally I don't use MPLAB as IDE so I can't say for sure.
4) Don't know. Hopefully someone else does.

/Henrik.