Of course there are always some mishaps, and in my case it was a weird case of internal shifting on a few of the parts. I don't know if this happened when the files were transferred over or what, but here is what the end results where on a few parts:
Pic 1: Holes line up, but pipe/rod holes are off-kilter
Pic 2: With the bolts in place to give a better idea of miscut
Pic 3: Hmm, looks a little off...
Pic 4: Again, center hole shifted off center (Z axis carriage)
Pic 5: So, as you can see the carriage is not center in terms of being level on the ground; however,
Pic 6: when you place the square on the internals of the carriage, everything is nuts on square.
Luckily the guy that I worked with to cut the parts is a stand up guy, he has been more than willing to recut any part that I need fixed - so I'm going to definitely get the CNC router end support plates (front and back) recut.
I am going to try and make the Z Axis carriage work. I think that it shouldn't pose any problem - I will likely just bore the rod hole that is off center to a larger diameter and install my anti-backlash assembly (reason being is that even though the center hole is off, the four bolt holes are right on; unless there is something I can't see, it should work out).
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Mike