take the y axis gear rack off and mesh it with the X gear rack. you should easily be able to see if its of inconsistent pitch.
as for the friction in the linear rails.. that's a lot more expensive to fix. clean them out..
"I have removed the track and ran the gear alone on it. Some areas did not run as smoothly. The same areas as seemed less accurate from the cuts. "
what does that mean? i interpreted that to mean the linear rails are stiff but you could have worn out that unhardened 1018 steel rack.