I have resolved the issue. The fix for this was two steps all contained within Front Door. This is assuming that plugins and apache are not causing issues with custom configured redirects.
1.) Go to azure front door designer and go to the backend pools settings
2.) Choose the backend rule that routes the traffic to the site/vm that is experiencing the loop.
3.) Input custom domain name that is experiencing the loop in the box "Back end host header", then click update.
4.) Go to the "Routing Rules" and choose the routing rule for the site experiencing the issue.
5.) click the drop down "frontends/domains" and uncheck the default url given to the site by front door, typically ends with ".azurefd.net"
6.) Click update, then save button in the designer.