I'm pretty sure the 68 heads have bigger valves and ports than the earlier ones on the 413. 68 heads should be the 906 heads which are open chamber, so you might pick up a little compression with the older heads buy I don't think it would be worth it. The 68 383 four-barrel cam is a little...
I wouldn't call the job "professional looking". Look at the roof by the windshield where they cut the rest of the roof off. It almost looks like duct tape finishing off the end. The top is likely from a 2 door convertible and so it does not fit all the way to the windshield. The 4 door hardtops...
Maybe, like you said, find a bolt that almost fits and screw it in, only use some JB Weld around it to hold it in and seal it. If the manifold was easy to get off, then I would tap the hole and put in a plug.