I was having trouble getting the smaller gears to print because of the overhang. I used OpenSCAD to fill in the bottom of the hole on each gear so that there was a clean bridge. I left enough of the hole to act as a guide for the drill. The scad files are created demonstrating how to do this.

The import feature in OpenSCAD provides a convenient way to make simple additions and deletions to an existing part if the only thing you have is the STL file.

Print the v2 versions of the gears, then use a 3mm drill (ideally held in a pin vice) to clean out the hole.