Great you cut your first part Peter!
I changed the native units back to good old inches, adjusted the motor tunings and looks fine
You should not change the native units at any time Peter. This changes your steps per., motor tuning, tool table, work offsets, etc. For example, if have a tool that is 3 inches long and .5 inches diameter when you change your native units that tool would now be seen as 3mm long and .5 mm diameter. This is not the proper way and can create quite a mess. If you work mostly in inches, the native units for the profile needs to be inches. If you ever need to work in MMs as your units just create another profile and make it's native units MMs.
You don't have to change your native units to execute code generated to run in MMs or Inches. As Ray pointed out, you will do this with a G20 for inches or G21 for MMs. Gcode is only units. A G20 G0 X5.0 will move your machine 5 inches. A G21 G0 X5.0 will move it 5 MMs no matter what your native units are set to and assuming your steps per are accurate. Did you ever get any numbers on your ball screws to use to set your steps per? Have a look at this link and you will understand why you need the specs on the screws I think. Screws with 5mm lead or .200" lead are very common and close to one another. A 5mm lead converts to 0.1968498" per revolution where the .200" is exactly .200. Sounds close right? Now, the .200" lead will take 5 turns to move 1 inch. The 5mm lead will take 5.08001 turns to move 1 inch so at 5 turns of a 5mm screw you will have moved .98424 inches. That's out by .01576" per inch and this will be cumulative so multiply that by your travel. If you command a 20 inch move that move would only go 19.6848". That's out by .3152 inches or just over 5/16 of an inch in just 20 inches. Over 40 inches that would double to just over 5/8 of an inch. I could cut closer with a band saw.
http://www.machsupport.com/forum/index.php/topic,12512.msg81001.html#msg81001Brett