The state of the floor looks familiar - mine was similarly holed. I will attach some pictures and also the pattern for the inner sill section that I needed to make. The section was inserted with a 2 inch offset between the joins on the horizontal and vertical surfaces to increase the strength of the join.
The full set of restoration photos are here:
https://picasaweb.google.com/108300898161301588285/FulviaS21600HFRebuildOne of the critical problems is the state of the bulkhead in the footwells - this separates the inner and outer sills and is the major attachment point for the subframe mounting box so it needs to be solid. If you need to replace it, consider removing the outer sills (which are readily available) and putting a plate between the inner and outer sills. This will make the inner sill a sealed box, so it is much easier to keep moisture out and waxoyl in.
Glyn