given most of the holes are going to be printed at an angle and we have no clue what printer you have or what slicer you are using or what settings you use....

A 0.2-0.25 mm clearance works well and allows for glue as well.

printing the rods is pretty simple.
What you do is the create a cylinder lying on it's side and then shave a mm or 2 off the base so that it lies flat against the printbed.
It will fit just as snug in the socket as a fully rounded dowel.
But with the advantage of easy printing and also printing in the correct orientation for maximum strength.

It's a really simple design.
2 parts - assuming all the dodecahedrons are equal.