Body work will be your most expensive cost, mostly due to labor. This is where you really need to think about what you want to end up with. I took my car to a shop that I trust and know does excellent work. I told them my car was their lowest priority and to work on it whenever they got around to it. They took me at their word. Everything was stripped from the car and every panel, seam, weld, and fastener was evaluated and corrected. Eight years later I have a fabulous paint job with all corrosion removed. The body is "flat" - you look down the sides and can't see a ripple or seam. Park the car by a window and stand with the car between you and the window and you cannot see the color of the car in the reflection from the window. All of the factory spot welds were reproduced when any bodywork needed to be replaced, and the minimum amount of steel was removed. Patches were taken out of replacement panels vs replacing entire panels. Very labor intensive, but the shop used the car as a way to work out techniques and processes for their staff. The finish is better than new. Sounds great, but that totally raised the bar for all of the other parts that go back on the car, so now I'm "that guy" looking for proper finishes and date codes for everything else. On the plus side, I am learning a lot more about these cars and the things I can do myself vs having to pay a shop for (although to be honest, with the number of times I have to redo something because it's not quite right makes the cost thing a wash - or worse). The downside is, the car has been off the road a lot longer than I intended, and there is still about 2 years to go. But damn - it's gonna be nice. Basically, beware of scope creep.
With your floors and trunk needing replacement, I would expect to see rust in the rear wheel housings, cowl, and core support. What you replace or repair will depend on what you want of the car when you are done. I would recommend anything structural be replaced, and anything that can lead to future damage (like a leaky cowl) be at least repaired. Anything cosmetic is up to you. All of these parts are reproduced to one level or another (cheap stampings from China on eBay to pretty faithful reproductions from Dynacorn). In general, the less you pay for the part, the more you pay in labor to get it to fit properly. If you are going to do any of the work yourself, particularly disassembly and reassembly, take pictures of EVERYTHING, from as many angles as you can, even of things that seem unimportant - like holes and brackets. Lay parts you take off on the floor in an exploded assembly view and take pictures of that, with closeups where fasteners go. Bag and tag anything that comes off the car. Don't get rid of anything until you have a replacement on the car, even if you are replacing them with aftermarket parts or upgrades. I like to group things by subassembly, but that's just me. Add notes to the pictures, and save them in folders that make sense to you and then back them up. Twice. They will become invaluable when you get ready to sign off on bodywork before the car gets painted, or you put stuff back together. A lot of the reproduction panels don't have all the holes put in them for all of the features of the car - like holes in cowls and firewalls for vacuum lines, brake proportioning valves, or any other option you have, the AC condensation drain in the floor, or various wire passthroughs, fold down seat supports, spare tire supports, etc., in the trunk floor panels. You can't always count on the body shop to know where these things go. And no matter how many photos you take, you will wish you had taken just a few more.
As far as shop selection goes, it's a bit of a crapshoot if you are going in cold. Go to car shows and talk to owners who have cars that look like where you want yours to end up and ask them where they got their work done and would they go back to that shop again. Then visit the shop and ask for a tour. Shops that do collision work as their mainstay have a different mindset from shops that do custom work or shops that do restoration work. I would recommend against a force fit between what you want vs what the shop is best at. Be aware that no shop can guarantee an estimate (time or cost) and Run Away from any shop that does. Old cars contain secret surprises that don't get revealed until the car comes apart, and by then you are committed to dealing with them. Most shops aren't doing this to mess with you - it just is.
Well that got a lot longer than I expected. I could go on and on, but I think I'll wait to see what questions you might have so far.
