Print the parts list. The separate files for gears 1, 3, 5, and 7 are just there in case you have a problem with the four gear plate, or if you want them in separate colors. Use multiply to print four of the pin pairs at once.

Plug the short pins into the holes on the small faces of the center block; plug the long pins into the large faces. Slide each gear onto its corresponding pin. I like to start at the top, because it's more obvious how the gears align with each other when you work your way down.

It's always difficult to calibrate a printer to make perfectly fitting bushings, but the good news is if your heart comes out too tight to turn nicely or so loose it's wobbly, all you have to do is make new pins. You can either regenerate them with different parameters from the scad file, or you can just take the existing pin file and stretch it as required in the various axes. This means the big prints won't be ruined by a miscalibration.