Wow, you've been burning hours on this today, that was a good thing to go through though.
Mach3 (if that's what you're using) is designed to run on ancient hardware - I wouldn't be so quick to point my finger at that.
What controller do you have and how do you talk to it (parallel or smothstepper, etc...)?
That pause you're getting on the X, is that always in the same place or is it random along the length of travel?
To cut the CAM part out of the troubleshooting process, I suggest you manually write a G-Code program by hand using something like notepad that moves the x back and forth, something simple like this:
G0X0
G0X12.5
for rapids
or this for feed/speed (that's for 90ipm, you might want to change that to metric):
G1X0F90.0
G1X12.5F90.0
Just copy and paste that as many times as you want to make it repeat in your test.
There is a way to make an endless loop in G-Code, but for testing - copy and paste is much simpler.
What I meant above was that the change in velocity is always in the same place, you most probably have a rail/bearing binding issue.
If it's random, it could be noise or about 101 other causes going all the way back through the motor, wiring, controller, port, to the computer and any anti-virus software you may have unknowingly running (hint!).
Pop the belt clamp off and run the test program again - see if you can hear that pause in the way the motor runs, that should reveal some more useful info already - see if it still does it...
What you did today was a good idea, I think we're getting closer to the actual issue now... ;-)
--
Mac
PS: I just remembered that yours the one with the squaring cable pulley system, isn't it?
Could that have something to do with it all?
If that problem jumped on you from y to x, that would totally indicate to me that you have a racking problem, no?
I would definitely recommend to take the plunge, buy another motor and go for the slave mod on the left side. As far as I remember it was only about an extra $70 total for the stepper, belt, pulley and the parts and took about one weekend labor to implement it all. To this date, I still believe that this was probably the best thing that ever happened to my machine. I do recall funky stuff like you describe before I did that, but once I had that second motor on the left slaved and online, it all these issues magically disappeared and I haven't had the slightest problem since...