I have spent alot of time looking at the stock body while hacking my rig to pieces. Some observations that might help you out:
Tying the cage B-pillar into the stock B-pillar, and still being able to get the doors to seal is going to be tricky (for the hardtop version). The softtop will basically eliminate this problem, though the top itself will be horribly complicated to produce.
If you are going to have a hoop (or overhead bar depending on your design) in the same plane fore and aft as the stock b-pillar, that overhead bar will be right above your head, and very close (it was too close for my tastes). It will definitely be too far forward for diagonal bracing in the same plane.
For the C-pillar, the same basic observations apply, except you also need to consider that your pillar will terminate at the inner fender - not really an ideal tie-in point.
But dont let any of that keep you from doing it. Figure it out, build it, and make sure to take alot of pictures.
Travis