Part it out.. because with the cash they give you with a low buyback, save what you want and part the rest. Im willing to bet the inner trunk metal is shot and would require some hours on the rack alone, plus replacing a quater is a tedious job and will cost a ton. Not to mention I can tell you everything on the drivers rear will be off, its hard to pull it back out, then cut the quater out and make a replacement fit again.
And to mrniceguy, nitto dr's suck a*s in the rain. Even brand new. The regular nt555's etc do fine. I know a few people who did the same thing, get caught in some slight rain, hydroplane and its all over from there, along for a ride.
To the op: Sorry about your car, but even a low number, after being branded rebuilt noone will care about it. Its a personal choice now, because there are 5000 other cobras with clean titles that will be more sought after. Not to mention if you fix, itll cost more than the car is worth physically. Personal attachment depends on the person.