To answer your question, yes there is a chance that it's a timing chain going...or more probably a guide or sprocket.
But you have to start with the basics. You need to check the ignition timing and you need to check to see if you can definitely nail down where the knocking seems to be originating. And you need to check the compression. If the valve timing is off due to a bad timing chain or one of its assembly parts, you should see that in the vacuum reading.
Ultimately, you may discover that the overheating did permanent internal damage and you need a replacement engine. But IMHO you don't yet have enough information to say that.