I’ve got a rough sixties 9ft mal that has had the original fin replaced with a box and plastic fin.
I’ll remove the box and glass on a D fin more in keeping with what should have been there.
What size base and height would be appropriate?
Cheers.
Can you post a pic of the board?
Don’t know answer to your question but I once had a '60’s Yater Spoon (rescued from a friend’s ivy beside his house), yellowed to beige foam, twist warped into it down the length. Got it free… Ground off the broken fin, put in box, and used a Liddle flex fin. One of my all time favorite boards. It was 9’6" and I’m only 5’3"X 120 lbs but it handled like a dream in small surf. The fin makes a huge difference in how it rides which I’m sure you know. The question then is…is it your goal to have authentic look, or best possible ride?
Unfortunately no fin is going to save this board, it paddles and rides like a dog. 
Just hoping to clean it up and maybe it will look cool?
So what size base and height would an average D fin be?
D fins were on the way out by 1965. The so-called “speed” fin can be found on some boards even before that. Your board may not have had a D fin when new. Hard to tell exact age of it with just the pics provided.
I’ve got an original Dave Sweet D fin at my shop. I’ll pull some measurements off of it for you in the AM. Your board probably did not have a D Fin on it originally. They are usually less than 9 inches in depth.