There were some replacement panels available, but they won't cover the entire area (i.e. not all the way across the transmission/driveshaft tunnel). They're "intermediate panels" made by Mr. Mustang, and I got them from CJPP... but it appears they no longer have them available (must've actually updated their website - lol)
You can see the new piece toward the top of the pic (passenger side). It covers the torque box, so you would need to put this piece in before dropping in the floor pan (if you're doing that much replacement). And of course, it's not a perfect match to the stock piece it replaces (some 'different' stampings), so it's probably not the best for concours - but, it'll fix the bad spot in that area at least.
I think I still have the driver side panel (ended up not using it). If it'll help, we could work something out - it was only $39 when I bought it last year. I'll post a picture of it this evening when I get back from the shop.