Wayne,
Welcome to the wonderful world of owning a classic Mustang.
Some free advice:
Slow down.
I've wanted a 67-68 since I was a kid, so I'm pretty excited.
Unless you're getting ready to kick the bucket, your dream car isn't going anywhere. Do it right the first time and you'll avoid wasting time and money.
I bought it sight unseen, so I'm sure I'm in for a few surprises when it gets here this weekend.
Trust me, you're in for a LOT of surprises. Based upon the description from the bodyshop you're looking at a LOT of metal work. Understand that it's unlikely that the bodyshop that inspected the vehicle understands these cars half as well as most of the members here. Building a classic Mustang is a fairly easy/straightforward process, but it has to start with a solid foundation.... the body. Before you spend a dime on "go fast goodies" like a TKO or 9", realistically, unless you do the work yourself you're looking at probably $5k in metal work. Since the drivers side floor needs to be replaced, this is usually a sign that the cowl is leaking. If that's the case, $5k will get you started, but you'll need more cash. The good news is it's only money. You can make more.
IMO, this should be your agenda:
1. Thoroughly inspect the car for any damage. Use this forum and the knowledge from our members to help perform this inspection. There's nothing that you'll find that we all haven't seen before.
2. Figure out if your skill level will allow you to carry out any of the necessary repairs or if you'll need to farm them all out to a qualified shop. If/when you do need/find a qualified shop understand that your "emergency" to get the car repaired isn't their "emergency". It's not uncommon for a really good shop to have your car in various stages of progress for months/years. You'll hear it refered to as "paint jail". Of course it can be repaired faster/quicker, but you'd better be standing there with your wallet open to make it happen. Based upon only the description you've provided of the bodies condition, a quality shop's repair bill to include paint could EASILY top $10k.
3. Dream about the days of going to swap meets to source replacement parts and when all you have to do is figure out the difference between a TKO600 and 500 and then buy one (by the way, it's an internal difference and can't be determined from the outside).
Slow down.
We can tell you everything you'll need to know and more... whether it's good news or bad.... but don't let your excitement over obtaining your dream car cause you to jump into poor decisions.
Also, since your car's coming with a 289 there's not a snowball's chance in he!! that there's a 9" rearend in it unless someone swapped it in already.