I think if I wanted the body up off the frame, I'd go ahead and shim the biscuits and get the body where I wanted it, then start on the bar/cage. I'd resist any ideas about including a flexible mount into the bar/cage structure. It will be ok to add structure to the frame to attach the bars to. I would just punch holes through the sheet metal floor of the body, build the bar/cage and then use large rubber grommets to form a seal between the bar and the body. The diagonal bars which support the B bar and run to the trunk area are usually run through the shelf panel speaker holes and will tie into the rear frame area as far to the rear of the car as you can get. It is perfectly ok to add some material to the frame in the rear area if you can't get the tubing in the place you want it. Add a crossmember between the rails to weld the rear diagonals to or whatever you have to do. Remember the rule, if the car is framed, the structure has to tie to the frame, not the trunk sheet metal.