So I managed to fix the main issue I was having with my unraid server (the proxy issues) so far at least....by doing the following in case anyone has similar issues:
If anyone has the same issues as I did above I fixed it by removing the containers (all relating to NginxProxyManager) and deleting the related folders in AppData, then re installed the NPM container and set up each proxy host 1 by one. So far its working flawlessly.
Still having the weird issue where the array doesnt want to restart without rebooting if I stop it manually, but I can live with that for now!