Manage Path Replacement???

[mcarlton00]

So I have to manually add all the paths to every shared drive, the same as if I'm just using Kodi to manage the database anyways?

In short, yes.  Path replacement was deprecated in in the server in the 10.9 release cycle, and it doesn't exist at all in release 10.10.0.  If you want to use native mode, it has to be configured client side.

In regards to your library selection issue, that's less clear.  I've never seen that behavior before.  If I had to guess, either there's something that's gone wrong in your authentication to the server so it's unable to actually retrieve library info, or switching between native and addon mode has made things go very screwy.  In the case of the former, I would expect there to be log messages within Kodi to indicate such an issue.  In the latter, there's no telling what you'll find in the logs.  Either way, I would think that doing a full database reset within Kodi would get things back to a normal state.