extrude perpendicular to surface & remove duplicate surfaces

Happy 2017! A bit late, but with heart.

I have huge problems, that even after I ran trough many discussions here and outside this forum, I couldn't solve.

First - why is Panels component (from Lunchbox) generating so many edges?

You can see that I want to check the volume of the "pipes" , but there are so many duplicates (or at least very close values) that it gives wrong results. How can I remove duplicates here? Vertices also have many duplicates, face might have too.

Second - how can I extrude the different panels (the ones in the end geometry, that are already rotated) such, so the extrusion happens perpendicular the each of them. I will cut them out of 3 mm Plexiglas, but I can cut it only in 90°.

Thanks to anyone that is willing to help, I already tried so many options and nothing worked...