Mike, if you worry about getting your money out of a thirty year old boat you'll go nuts. Make it the boat you want. I bought my 45TF as a project boat too, and will spend much more that it's eventual market value before it's done. So what! When I bought it I told my wife it was the model I wanted, the hull I wanted, and it had the engines I wanted (8V71TI's), anything else I can fix.
For your dinette, take a look at the open 36 interior photo on the "rare commander" thread.
Your portholes are probably the same as those on my boat - the cast aluminum ones about 26 inches long with three dogs to close them? If you are in salt water they are probably a mess. There were four for sale on ebay a while back and I think they went for about 25 bucks each. I do know a guy who might have some - I'll check and let you know. I pulled mine out of the boat and completely rebuilt them - new tempered glass and everything.
Here is a two-page Chris-Craft ad about building tournament fishing boats: