Re: p&b shakes
You can do both at the same time. My advice would be to start the PB shakes first and do them for a few days until you're sure you've got things moving somewhat regularly down below. You don't want to start detoxing and stirring up a bunch of filth, and then not be able to get rid of it because your bowels are stalled out. Make sense?
Beyond that, I would take your actual herbal detox/vitamins/supplements/food either 2 hours before or 2 hours after a PB shake. You don't want it absorbed by the shake and shoved out the other end without being absorbed, or it does you no good.
Every body responds differently to a cleanse, but several BM's a day are possible once you get things going. Headaches and other cold or flu-like symptoms are also possible.
Lots of water, yes! And you might consider an herbal laxative in the evening to help keep things moving.
As for whether or not you can cleanse while you're ill, I honestly don't know. Sorry!