Considering the car was 'restored' I was hoping that the sill rot was just on the surface...

But, as you can see here the sills were made up of layers of plates, fibreglass and filler. The top image is the paint ground away, and the bottom one is the skin cut away, revealing some pretty rusty inner sills.

Another view,

The guys at the bodyshop reckon they can fix it all up, and although I don't know a great deal about this type of thing I trust them. Strangely the rot seems to stop at the door, and the sill there looks good and original.
They have asked me if I can get a good side image of the rear quater panel that they have had to cut away, mainly because of the small feature line that runs the length of the door and quickly dissappears into the rear fender, so if there are any other barracuda owners out there who can get me a close up picture of this feature I would be very grateful. Also was there a visible seem between the sill and the fender on the original or would it have been filled?