Not sure how much it lines up with your specifics but I've used Neutron for ages and it supports WevDAV, SFTP, UPnP/DLNA amongst other things and sounds great (to my untrained eats anyway)
Thanks for the input everyone, I think I'll go with rolling apps and OS into one drive as that seems inescapable and using fstab to mount my games drive inside /home/USER/ with a media drive left as just a drive. That leaves me with my smaller drive for Windows and a spare OS agnostic drive for both OS's to access.
Thanks for all the advice everyone, we're taking these suggestions on board and we'll keep working with him to get a handle on things