Primo Perpendicularity Problems

I have just got my new smaller Primo assembled.
The first thing I tried was to check for perpendicularity, and what I found was frustrating to say the least. The Y+ X- direction was 2.45 mm higher than that of the opposite corner that is across about 7 inches.
after some quick searches on the forums I found another post like this one where they where being told that it would be unnoticeable. Reading this I decided to give it a try the way it was. first things first I try to surface my spoil board here is the result…(see pics) Definitely not acceptable in my book. which brings me back to the main reason for posting this. What adjustments can be made to help bring the z axis into spec. I am pretty sure its in the z because the rail corners have less than a 0.2mm tolerance, and the center gantry sits level to the spoil board measured from the bottom edges.
I did however print my Makita mount on a different printer than the rest of the build, I doubt it but, maybe an issue?
The surfacing has been done with a 12.75mm carbide slotting bit.
The feed was 4000mm/m
10-13k Rpm
0.5mm DOC

The X axis lines


A close up

The Y axis lines

A close up

A shot of the whole machine.

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Update:
I checked the z tubes for “wobble” low and behold they where like a Tater Chip. After squaring and tightening the tool mounts down while it was still on the glass the unevenness was down to 1.2mm over 7 inches. With a bit more fiddling around I was able to tweak the z axis making the unevenness seemingly negligible. I haven’t had time to take a test cut yet.