mrpdean

From my experience, making large scale changes to the exterior Tamriel navmeshes is tricky. As a general rule, you don't want to delete the existing navmeshes as this will lead to the sorts of problems you've described. Instead, you either want alter the existing navmeshes to suit the changes you're making, or I've heard of some people moving the entire navmesh of a cell well below the ground level and creating a new navmesh in it's place, at ground level. Either way, the original navmesh remains. You can basically delete all but one triangle from the existing navmesh, and then just start to recreate it to suit your needs. Because you're starting from that one original triangle, the CK won't change the ID of the navmesh which I believe is the important part. I'm no expert on this but just thought I'd pass on what I've picked up along the way. Good luck!

No mod that I'm aware of. Bugs me that this was not implemented as well. There are a few examples of how to do this on a per bed basis and I played around an managed to make something that worked for my own mod house and custom NPC's but I don't think anyone has managed to do it on mass, across all beds and NPC's in the game.

I'm new to this forum and a little blind at times so I'm not see any attached screenshot on your post, but if the problem is that the color of the face is off in game, then it's generally because you forgot to export the Facegen data.

Did you remove to collision data from the mesh, using Nifskope?

I see. In that case you will most likely have to assign the normal map to that mesh using something like Nifskope. Where did you download the armour from? I could take a look at it if you like.

From my own very limited experiments with creating/texturing assets for Skyrim, the shine/specular look seems to come from the alpha channel stored in the normal map. At least that worked for me when I remodelled the oven from the Hearthfire DLC. Added an alpha channel to the normal map, white area's got full specular, black area's got no specular. might be work a look.