I purchased a 65 coupe. Had it a couple of months, knew I needed floor pans, so I ordered them from NPD. Had to move car from town to farm (uncle'). He has a car hoist. This is the first time I had actually seen the underbody of the car. Needless to say I was having regrets but could see potential while putting a hole in my pocket at the same time. All the frame rails, rear tourque boxes, trunk floor, possibly inner rocker panels need to be replaced. I also need to replace front and rear aprons on both sides along with shock towers. I guess I just need to know where to begin. This is a std 65 coupe 6cyl auto. Any recommendations are appreciated  

Start over.  Find another car and use this one for parts or sell it.  You can find a solid 6 cyl coupe for less that it is going to cost you to fix this one.  You have listed a lot of metal that needs replacment.  Your cowl vents are probably shot, too.  

Welcome to the forum. Frankly, there's nothing special about your car that warrants to amount of work you've described that need to do. If it was a rarer car it might be worth it.  Based on what you've said, you'll have 10-15K in it in just fixin the sheet metal. If you have the necessary skills your cost will go down, but i'm not sure I'd call this one "a diamond in the rough".  You can buy much better starting points for under 5K.  IMO -This one's time is up, sell it for scap and move on to a new base.  

These guys are right,,,sadly. People just dont realize how much time and effort you can put into these cars. The thing to remember is that it costs the same to restore a six cylinder coupe as it does a V8 convertible and what do you have when your finished ???I have seen lots of people do that ,,,I mean spend a fortune on a car that isnt worth it, but you can make a choice now. If its really what you want, go ahead and enjoy the work. Just enter into it knowing you will never get anything close to your value back when you sell it. There are few cars that return the cost of a restoration,,,,dang few !!!! But at least you enjoy them while you have them and get something back from the money.
If you do continue, I suggest you start with the floors and inner rockers and go to the front and rear sub frame then do the trunk and lastly the shock towers. Whewwww ,,, it hurts to even say that.  

I just wanted to thank you all for your input. And I think I will have to part it out and sell it. You know your driving down the road and it catches your eye, it calls out to you, you think not bad I can fix that up, then u see the underbody. Ya, find another one I guess. thanks guys. I love this site.  

I am gonna give you a story and you do with it what you like. My wife and I helped our son buy a well used(crappy,rusty.beat) 1966 six cylinder coupe in april. He is 15 and wanted a car to "work on". It needs floors, trunk, wheel houses, quarters, ect ect,. I intentionally bought a six, I wanted it to be a learning tool for him. He is learning to weld, use a chisel,cut off wheel,grinder, DA sander, what an engine is, how it works, and a whole bunch of other stuff. When he gets it together he will have a decent car that cost a whole lot more than he can ever get out of it finacially but what value does an education have? I wanted to let him make his mistakes on something that didn't matter. I also understand the possibility that this car will end up around a tree some where. I hope he gets a GT, or Boss, or shelby someday, but I don't want him to use those to practice with. If you want to try being in the Mustang hobby maybe a "practice car" is the right one to start with. If you don't know how to weld, have never done any bodywork ect, ect, and don't want to learn..GET RID OF IT, if you think this is something you might want to do as a hobby for years to come a six is just as good a project as any. In my sons case it will also keep him broke and in the garage(where I know what he is doing) for the next couple of years.  Good luck. Tom  

Very Good points Tom.  It's really the owners call but some of the aformentioned experiences may come at a cheaper price in the future.