Is this a possible configuration to have Jira/Confluence reside on a new in house server and connect via SharePoint Connector to our external hosting provider? They (the external host) have our SharePoint on their server.
Yes, it is possible. However, both your Confluence server and SharePoint server will need to be able to access one another on whatever ports are being used to serve up the sites. If one or both servers are behind a firewall, you'll need to set up a rule that allows traffic to the other server.
You'll also need to make sure that your external SharePoint hosting service permits the installation of custom SharePoint solution files (as this is a required part of the installation process for the connector). Additionally, it must be a full -blown server installation of SharePoint. SharePoint 360 and SharePoint Online are not supported.
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