My first calibration print of the pyramid, although great, was not perfect. Although you cannot tell from the angle of the picture
The object was slanted in the X axis. Stressing out that the shifting would be on of those problems that you just couldn’t fix, I started inspecting all the hardware again during another test run. What I noticed was that my GT2 timing pulley was slipping whenever there was the slightest bit of load on the x axis. Realizing that the grub screws had come loose, I immediately tightened the grub screws and voilà! On my next print, the x axis was no longer shifting and I had near perfect accuracy with my prints.
When measuring the Custom Calibration cube, I noticed that I CAD’d the model to be a 1 cm x 1 cm cube but the end result was approximately 1.17 cm x 1.20 cm. A question that I encountered with the Makerbot that I worked with at Berkeley was does the printer/slicing program print along the lines or slightly inside to compensate for the filament width? There are settings in the slicing programs to set filament height but never settings to adjust for filament width after extruded. There might be but I either haven’t seen it yet or recognized it yet.
Now that I feel somewhat comfortable with the quality of my prints, I shall move on!