Thanks for replying here, because it's a good reminder for me to update this post!
It looks like we've at least partially debunked the Damon KNOWLES theory through the Bahamas DNA Project/Bahamas Genealogy Group. Everything I know about James KNOWLES at this time can be found at
http://www.geni.com/people/James-Knowles-Sr/6000000013538327...It's certainly still possible that there's a Bermuda connection, which would make sense given Bahamian history, but it doesn't appear possible for Samuel to have been James' father. Thanks for your offer to help!