If it is a combo of years and not original right now just build it the way you want. The value is only what someone else is willing to pay for it. How much would it sell for right now? How much would it cost you to restore to a point where it was a collector quality car? You will never get out of it what you sink in it. Build what you want and be happy.
Personally I would rebuild what is there, stick a manual trans in it and drive it. Keep the Ford drivetrain in it. (that will help the value down the road no matter what.) The Caddy motor and GM trans will not do you any favors in the value department. And you can get a HUGE amount of torque out of that Ford motor that's already in it.
It's your car, build it your way and have fun.
EDIT: I had more thoughts. I am wondering why you want to put the 500 motor in it? Is it the "dare to be different" factor or is there some performance you hope to get out of it that a big block ford will not produce? And the C4 suspension. It was designed for the corvette. The balance, weight, dimensions (and needed modifications to fit it) are way different than that Mustang could ever use. My point is that yes, the suspension is a decent one. But only in the right application. That Mustang is not the right application. Then add a 500cid Caddy motor on top of it and you make all the problems even worse.
My thoughts are just that, thoughts. I may be wrong and maybe you are onto something i am unaware of. But it would seem to me that using the Cad motor and vette suspension is a very expensive and time consuming operation with a worse handling car that has an even lower market value in the end. In other words you are wasting your time and money and not getting any performance or financial gain by doing it.
That car will handle better, stop better and just perform better with modifications to the stock drivetrain and suspension. It will be worth more in the end too just in case you ever hope to sell it.
Just my opinion.