Lunchbox fail

Hi, I am using Lunchbox in order to create a truss inside a certain shape. However, since I have different variables that changes the shape, it ends up having a lot of duplicates and lines with 0 length.

Is there any way to solve this problem. Or maybe there would be another way of building the truss?

There reason I need to do it, is because it result with invalid extrusions thus not everything is bakeable. Plus when i try to thicken the interior truss elements ( hinv a sort of volumetric sheets instead of flat ones or lines if you where to look from the front side)

Thank you for your help or any answer that would help me solve my problem .

Here is the problem I got while extruding, where's the thickening didn't work at all as I need it to...