So i'm technically back to where I was a while ago. However this time I've changed the wiring to use the aviation connectors and i'm using the new enclosure so can see how much current the motors, Arduino and fans are drawing when in use. A useful test I think.
I had to take the gantry of the rails and try and sort out some issues with the rails not moving square. I've checked the diagonals and they are within 2mm of each other and both sides are the same length so i'm pretty happy with the main frame.
There is definitely something not sitting quite right somewhere though and I think it's possibly to do with over tightening the parts as it was originally being put together. Several of the pieces are showing signs of de-lamination.
This is running a lot smoother and a lot quieter than it was previously though so I think taking it apart, re-measuring, re-aligning and not over tightening it back up has definitely helped. Hopefully when the endstops are wired in, this will sort out the last bit of "out of square" when the axis are homed in.