How many circuits do I need and can I bundle wires in the wall?
I'd agree with Keshlam, ask the local inspector about that specifically.  It sounds to me like you don't plan on taking out a permit, which I would probably recommend, it gives you peace of mind knowing the job is done right, it's not very expensive, and you can tell the future homeowner when you sell that it was inspected and done to code.

As for circuit design, you said 6 circuits could be a limitation?  Then what I'd think about doing is:


Both bathroom lights on one circuit 
Bathroom GFCI Receptacle
Bathroom GFCI Receptacle
Largest and Smallest bedroom Receptacles
Two other bedroom receptacles
All bedroom lights (Assuming they don't exceed 12 fixtures)


You probably won't want to have all the lights from one floor on one circuit, as if that circuit ever trips, you'll be in the dark with no supplementary light to guide you.