Congratulations Bill! Just remember that you've not bought the "perfect" boat, but instead one with a lot of character.

I suppose that your boat has the standard Becton hatch at the bow; if so, you can probably get another hatch cover via West Marine or somebody like that, though you may have to buy the whole hatch assembly. The porthole and tube undoubtedly led from the rudder pedal once attached to the right-side Yakima footrest, to the now-gone rudder. There should be a socket at the stern where the rudder was once inserted. It might be a fine idea to re-equip the boat with a modern rudder. Regarding painting the boat, I don't see why you couldn't, but I'm no expert on painting fiberglass boats. The boat identification number and date of manufacture should be scribed onto the stern.

Have a blast getting your Dirigo into shape for the coming season. I envy your opportunity to repair/upgrade/modify the boat, starting from scratch. Let us know how it goes.