Tim, you have some work ahead of you but if your like many of us Mustang fanatics, its a "labor of love"
Everybody sells the sheet metal parts you are looking for. However, some of the cheaper stuff from overseas is usually a thinner metal. its okay but for anything structural, you want the proper gauge metal. I bought most of my stuff from "Goodmark". You can also talk to people like Kevin at Laurel Mountain Mustang. He can tell you what works and what does not.
Books are no problem. Laurel Mtn Mustang sells the various ford assembly manuals for the mustang by year. Its a combination of large page books ( 4 or 5) for each year and will cost you about $80 for the complete set. They are worth their weight in gold! However, you will still require a more detailed manual and information not covered in those books. I bought a CD on Ebay for $15 that had the ford assembly manuals / illustrations from 65 - 72 in PDF format. Again, another one of the "best investments" I ever made. Would have never have figured out how to get my door glass re-installed without it.
One additional book suggestion is one you can also buy from Laurel Mtn mustang or even Amazon.com. Its the handbook of mustang restoration. I strongly advise you get it becuase it will help you alot with the do's and dont's regarding how to do your sheet metal. As a matter of fact, make sure you have this one above all others. It will prevent poor decision making on your part and regrets after the fact.
You say you need to replace your floor boards. Many would think replacing the entire floor pan is the best way to go. But, unless you have access to proper jigs and fixtures, you dont really want to this route. Leaving your transmission tunnel intact is extremely wise. Get the book, then develope your plan. come to this forum and ask any question you need help with or suggestions. you have a lot of experiance from people here who have "been there /done that" experiance.
__________________ '66 Ragtop, vibrant red, 289-4V, 4-speed toploader
'68 Fastback, space blue metalic, 351C-4-V, 4-speed toploader | 
