Since all your measurements were undersized, if it isn't a line selection issue it could be a loss of steps for some reason or other. Low pots is a common problem, but another very common one is loose or missing pulley screws. If one screw isn't tightened in the dead center of the flat on the shaft, the shaft may be turning slightly before it engages the screw. The screws can easily work their way out, a lot of people apply a little bit of low- or medium-strength loctite to them.
Another possible problem is improper belt tension. Too high and the steppers lose steps because they require too much torque, too low and the pulley could be slipping past the belt. One good forum thread for mechanical loss of steps is https://discuss.inventables.com/t/guide-offset-cutting-lost-steps-positioning-errors-etc/16084.
You can find Machine Inspector under Machine->Advanced in Easel. The default settings for the step/mm usually seem to be pretty close to accurate, not as far off as the numbers you gave earlier, but it's something that might be worth looking at. I believe the values you're looking for are $100, $101, and $102. I know the X and Y for my machine were 40.0 by default, and the Z is dependent on which lead screw you have.
I posted a video on doing the step/mm calibration, it also shows how to get to Machine Inspector: https://discuss.inventables.com/t/x-carve-maintenance-troubleshooting-videos-add-your-own/13405. There's also a video in there showing how I measure belt tension on my machine.