No, you can't use JomSocial's Facebook integration and JFBConnect's integration at the same time. You'll need to remove the API keys from JomSocial, like you said you've done.
As for using CB and JomSocial together, as they mostly work independently of the other. I don't think you should have conflicts with CB, JS, and JFBConnect, but I think it would be hard to manage all the different aspects and prevent a user from updating the 'wrong' profile. Our demo site uses all 3 without any issue, but I wouldn't consider it a 'real' site.
After your explanation of how you're trying to work, I'm not sure what community page you're talking about when you say:
What I want to be able to do now is replace your modules on the community page and disable the jomsocial resgistration page altogether.
The page below may help, if you know where you want the Login With Facebook button, but if not, explain a little more what you're looking for, and we'll help you get there:
www.sourcecoast.com/extensions/jfbconnec...estions#login-button
Thanks!