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Rebuilt the timing belts using steel wire instead of cable ties to remove the slack. Made them all the same length and measured the ends to be consistent.
Test print shows the same problem however by amount but not percent. So this time the total discrepancy was 3mm over 400mm. The X axis is 100% correct.
One thing that had changed since my initial work was the use of a new Arduino due to some end stop issues. Using the original Arduino shows only a discrepancy of less than 1mm. So there is a setting that is different between the software on the Arduino causing the problem. The old Arduino still has a problem with the end stops and I cannot seem to get it to print as it always starts the print by raising the print head. Likely due to a home gcode.
How do I get the exact software for the Arduino that was on the one purchased?