Dimensions Slightly Off

Losing steps should be quite easy to hear
if you run your program cutting air and with the
spindle off.

To verify that its not a mechanical issue that has crept in,
can you still run the old controller?

Sorry about the .hal and .ini. Try these:    

Drivers being used are old Troy (chinese) drivers (that worked fine with the old RichAuto controller): 

User manual here (drive file because it's too large for forum limits):  drive.google.com/file/d/1BSWBPFRsO2LLnaD...kK4/view?usp=sharing

I did switch the X and Y axis steppers and the issue still happened on the same axis.

I can hear steps being lost while it is running, just not sure why they are being lost. I've tried each microstepping value I can, and I get the same problem.

I could try the old controller, but I'd like to do that as a last resort because that would take quite a bit of time to set back up.

I did tighten all mechanical connections.

-set microstepping to 1/4 or 1/8
-set the current .... it can not be set!!!
-set the acceleration in the ini file to 150 or 200 or max 250
-do some tests
Attach pictures of the machine here.

That looks like a CAD\CAM issue.

Can you post the gocde file ?

Also I note that the hal file is not using the "reset" mode
which will half the possible step rate. The hal file is quite old 
(LinuxCNC 2.7 vintage?)

Current stepconf uses reset mode, not sure when this was changed
Note that with you 51000 ns base thread and not using reset mode
the step/step jitter is relatively huge at full speed, that is step to step
at full speed might be ~100 usec one cycle and 150 usec the next

Another possibility is that if the error follows the axis and not the drive,
there is something funny about the X step parallel port pin, or the signal
path is marginal some how.