Okay. None of the holes are exactly 3mm or 8mm so don't use them. Even the bearing holes are 22.1mm. I would use the arm cross section as a reference. It should be exactly 25x25mm.
BTW, I just downloaded sketchup to see what is going on and there is no native way to import an STL. How are you importing?
That is nice! You can also use a tuner. It is important to note that you will need to keep adjustments very small or you have to completely redo your calibration table.