QUOTE: I'm thinking a non #'s matching running car with rust will fetch $5000 (am I way off?) And the same car with a fresh coat of paint, new body panels will get about $10k (again am I way off?).
You are correct to a point depending on how much rust. And if you price what it will take to get the new body panels and paint you might be as much as $5K in the hole......
My advice is to put all the good parts on the good body and sell the other with as little work put into it as you can. That way, if you don't get much for the rusty one then you will not be out as much time and money.