Success! And I must say that although support was not as quick as I would have liked, the service and tech was excellent.
I mentioned that i was a tech during the phone conversations where they have you tell them again why you need help (which I hate because I have already crafted my complaint and often my steps to fix said problem.)
As mentioned by @scottalanmiller and possibly others, SharePoint and ODfB has a list of file extension that can't be used. However the tech said they don't really have an updated list of what is bad. Example this list doesn't show .htm, .html, .php however he has seen these files work or gum up the works.
The fix?
- Stop ODfB sync client.
- Copy data elsewhere since the stuff on the harddrive was the known good master list.
- Delete the folder that was associated with ODfB
- Delete all files on ODfB website (O365 admin dashboard) except my OneNote files
- Click Sync from ODfB website and confirm that the OneNote Notebooks synced
- ODfB showed up in File Explorer
- Start adding one folder at a time and watch/wait for syncing. Zipped every web file to make sure they weren't going to hang up the works.
- All folders and files have been synced
I had to talk to the manager after the incident was resolved and was told that I would have the tech's contact info and to contact him for ANY Sharepoint/ODfB issues, even for my clients. Wooo hoooo!