It's always the case, things coming down to the wire and the most complex system in the game decides to not work. I have been trying to get my Nav mesh surfaces to correctly generate for over 4 hours not and am just not getting anywhere with it. Instead I am just going to have to remove hostiles from the game and settle with what I have got.

Hopefully I can cobble together a semi-decent game with the bits i've got left but this needs to be a lesson for both project management and scope management.