Thanks for including the Sketchup file. I'm new to Sketchup, but I'm trying to modify the top A2 and Base A objects. I did the modifications to top A2, but Base A is giving me a nightmare. I'm working on the corner closest to the 40 pin header, opposite where the Stem would be. I'm not sure if that corner is a nightmare, or I'm just that much of a n00b. However, the corner by the HDMI port was easy to do what I wanted.
In my Googling, it seems that there are plugins/extensions are commonly used, and some people say that you need to be running extensions. Do you use any extensions? Does the original maker?
As for what I'm trying to do: I'm adding screw holes, support for the board and new holes, making the lips flat (instead of like a stair), make the cover thicker, and add a cutout for a heatsink.