Z Axis Lifer Rods Not Lining Up #48

When I printed the rods out and tried to stack them, I noticed the connection point is not exactly flush or smooth at the connection point where the rods are stacked. I am currently having issues with finishing my printer because my sled gets caught at this section prohibiting me from printing tall prints.

I moved the rod into modeling software and stacked a copy of itself on top and noticed there is an overhang as shown in the images below. Is this an issue with the model? I know we have to re-generate the files using Open Scad, could this possibly be an issue that resulted from that?