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Sorry to bother you Ben,i found what i was looking for.At the start of the code use G29 S1 command to use the bed mesh level from the file when printing.Took a bit of reading to find the info,now i know a lot more about the G-code.
I still not been able to calibrate the machine in perfect square, i guess i will have to dismantle the X axis guide and remount it again in perfect square with the Y guides.(That's 2 days of work )