How bad are your floors? New floors definitely need a little massaging, so if you don't have to, I wouldn't replace the entire floor.
240Zs have an issue with the floors bending up when people use the subframe as a jacking point, but 280Zs don't really seem to have that problem. The rails under a 280z are much stronger, and so is the floor, so even though my rails look like they're caved/bashed in, the floor is pretty much perfect. But the reason I suggested leaving some of the original floor, is because bad dog's 280z subframe rails don't have a flange like their 240z rails do. I am certainly not an expert on the matter, but if you think about it a bit, having the flange there definitely seems like a good idea since whatever load/force the subframe rails put on the floor is more spread out.
If/when I ever get to the point of doing my frame rails my plan is cut off the stock subframe rails and leave maybe 1/2" to an inch as sort of a flange to weld the bad dog rails to, using spot welds, vs just butt welding them to the floor. I don't know if that's the "right" way to do it, but it seems better than butt welding them.
That's my take, for whatever it's worth.