Floor pans are not an unusual thing to replace in a mustang, let alone a rag top. I would only be worried if the frame rails were severely damaged by rust. Your inner rockers look good from what I could see. Check your torque boxes for punch through rust as well. Fortunately for me, I only had to replace the driver's front and passenger rear pans in my vert. Keep this in mind- nobody makes a replacement convertible seat riser (what your seats sit on) so you will have to reuse the old one if you go with full length pans. Do you have the under body stiffener plate? It bolts underneath the seat riser under the car across the drive shaft tunnel.