Even though I posted in your other thread here are my suggestions, and these are all from personal experience with my 65. BTW I can't find a pick of it completely torn down but here is one of it on the trailer heading from one shop to another to get the body work finished and then paint.
Get it running and driveable. Then you can really know what needs to be fixed mechanically. And it will probably be quite a bit to do. At a minimum all of the rubber and soft hoses will need to be replaced and probably all of the brake wheel cylinders and calipers, if it has discs, will need to be done.I wouldn't drive it without thoroughly going to through the brake system, not even a test drive. I know it is tempting to take it for a spin but try to resist.
To do all of the sheet metal work that probably needs to be done it would be best to gut the car. Save what you can and make a list as you go along of what you will need. I know that you said that you have a list of the big parts you need. That is the easy part. The little stuff WILL nickel and dime you to death, trust me on this. Invest in cheapo ziplock bags for all the hardware and label the bags with marker. It will make your life much less frustrating when you go to reassemble stuff. Like I said in the other thread parts are pretty plentiful for these so you really shouldn't have a hard time getting parts and that one isn't a really rare car, i.e. Boss 351 or a 429 car, so there shouldn't be the issue of hard to find NOS only parts.
And most importantly your budget for parts and such. Figure out what you think it will cost you and then double it. Then you probably have a pretty realistic budget. I was in your shoes once. I got my 65 when I was 15, drove it til I was 20 and then took it apart to restomod. That was 14 years ago and it is finally coming back together. Mostly due to money, or lack thereof, that and I am ADD when it comes to car projects. I start way to many at one time.
And one more thing. When you drive the car watch out behind you at red lights because you WILL put it in reverse at least once because you think you are in 1st. Damn Ford 3 speeds.