Created a simple desktop tool organizer. There are 6 separate files if you don't want to print it all at once. Pieces will snap into the base except for the SD holder which is a loose fit so you can move it around.

Created in Fusion 360, I included the Fusion model file and an IGES export so you can modify as you would like.

The bottom 3 mm should be set as solid to make sure you don't break through when dropping tools into the holder.

Update - Added a second SD card holder with a better use of space.