The self tapping screws will work in combo with the 3m seam sealer.
The question is, will it be able to pass state inspection after you patch the holes like that? In Pa. the inspection laws have changed, and they state that if you can visibly see a patched area either in the cab compartment or the frame, then the vehicle is no longer inspectable. The reason that the floor pans that you buy are pre-stamped and go from 1 seam to the other. To be welded in.
Just letting you know before you put all kinds of time and money into it, and have to turn around and have it done right. Maybe your state is different. Laws vary from state to state.
'87 YJ, 4.2L built and bored, 8.5" of lift, 8.8 rear, AX15/NP 231, Tom Woods drive shafts, Flat fenders, 12,000LB winch, Custom bumpers, Rattle can paint job. Never completed...