Hi Jim,
This is one way of setting the controller in line with the part however there are limitations when taking this approach.
I have used rotation to switch a part already clamped on the table with the datum in the wrong axis, rotated the G-Code using the rotation field by 90 degrees which works fine but if you need to "Run from here" I have seen the pre-run to the position will calculate what I assume to be a non rotated position and drop your tool into the part at the wrong location. If you have made a small rotation adjustment to match the out of line component on the table the difference will be difficult to see. The X and Y zero point would have to be calculated if not at the work datum edge, so setting the position would also be difficult as the zero datum would only be at the zero point at the program datum point. As Mach3 seems to not calculate the "Run from Here" on rotation it may have other aspects that might cause issues when in rotation, one of course is that you can easily forget to remove the rotation parameter on a job that is square to the machine.
If you are not cutting the whole component the whole profile, the best way to square up a component in the X axis is to use a clamp on one corner half tightened and run along the X axis with a DTI and gently tap the component until that face runs parallel with the machine access and then tighten a clamp at each end of the component. I have been in engineering for a long time and setting a pre-machined part or reversing to machine opposite side is the most time consuming part of engineering. therefore the most critical part.
Other technique's for machining the other side of a component with X axis location lug or a reference hole and a parallel to place the reversed component fall into the same category as your problem.
In summary the rotation is ok for the occasional incorrect set-up but be very carful and remember to remove the rotation parameter after the job is finished.
Hope this helps
Regards,