Hi,

the Joomla template in use doesn't impact with JAmp and it's not relevant. Indeed the template is completely skipped and stripped out when an AMP page is rendered.

For the menu selection, refer to the PDF docs paragraph: 'Menu, sidebar and modules'

Not sure about what's happening with your links.

Finally, jfbconnect should be a plugin if i'm right, there are settings for exclusions so you can disabled plugins. If this was not enough, there are settings for tags exclusions, selector exclusions, etc

Cheers