OK, so lets see what your problems are exactly;
1) You are having odd model damage occur
2) Nano FX is not working right
3) Your damage textures are not what you thought they'd be.
Right?
ok, so
1) this first issue is casued by faulty _vox files, occasionally you should delete all the files ending in _Vox.nif. BC will generate new ones, which should look better.
2) How exactly is it not working?
3) NanoFX does not use the stock damage textures, I think those are the stock ones, I might be mistaken though, as I haven't used the stock ones in a long time. most likely, this is connected to NanoFX not working, if those aren't the stock ones, I would guess that the textures you thought you installed didn't replace the correct ones.