I see, sounds like u didn't have time. I'd recommend for game jams just making things super simple, short and sweet. I think you tried to go very story rich and ended up spending time on things that aren't going to make the game engaging with the theme. But maybe this project will be one you keep working on and make better!
For nav meshes, a little hack I've found, if you just need 1 big flat mesh on a map just chuck a plane just ever so slightly above your entire ground and add the nav mesh surface to that, make it cover your whole map. It'll still cut out walls etc but it will be just a flat plane, will be much smoother! I did this for a jam before as I was just spending ages trying to get the nav surface flat.