Just like a few others I had a ”gap problem” between the front plate and the left X-axis plate when pushed all the way to the front. I could get the base squared by measuring the distance between the Y-rails and then measure the diagonal distance. It was spot on. But the gap was still there.
At first I was pretty confident that I could fix it real quick by following the official guide and reading here on the forum. But after 10+ tries my confidence was a bit damaged. 
So, I figured that I would try to find the source of the problem and disassembled everything. The X-axis plates came pre assembled and I saw that you could buy maintenance parts in the store so I stripped both plates.
I hope this can help someone else.
The front plate and the back plate had a tiny twist. When they lay down on a flat surface you could feel / hear it when pressed on the sides. That was fixed by hand, carefully twisting it in the opposite direction.
The front plate and the back plate had a small bend in the middle. When they lay down on a flat surface and the front is facing down (imagine the extrusions standing up) you could see some light slipping through in the middle. Same thing when they stood up (as they would with the waste board attached). All the screws for the waste board went in fingertip easy except the ones in the middle. They did go in easy, just not fingertip easy, so I can’t imagine that this need to be fixed.
The X-axis plates also had a small bend from top to bottom. The left one inwards and the right one outwards. I don’t think this need to be fixed since it’s 0.5mm across and it’s from the top to bottom. It can be corrected by leveling the extrusion.
The sides on the X-axis extrusion was not square. When it was mounted to the plates I had a 2mm diff across the whole length (measured from the left plate) and a 4mm diff across the whole length (measured from the right plate). I temporary shimmed it with folded foil so I could keep on but I will take it to a machinist to fix it for good. Now the diff is about 0.2mm on the left and 0.3 on the right (across the whole length).
After I shimmed the X-axis I did another assembly test (checked that the base was square first) just to see if there would be any difference. The gap was now on the right side. Meh…
The sides on the Y-axis extrusions (both) was not square. Right now I don’t care about the top and the bottom. Both diff a little bit but I correct that when I mounted them to the front/back plates.
The left extrusion had a 4mm diff across the whole length measuring from the inside/front and a -3mm diff across the whole length measuring from the inside/back. The outside had a -3mm diff across the whole length from the front and a 4mm diff across the whole length from the back.
The right extrusion had a 3mm diff across the whole length measuring from the inside/front and a -2mm diff across the whole length measuring from the inside/back. The outside had a -3mm diff across the whole length from the front and a 4mm diff across the whole length from the back.
The left extrusion length at the inside/top (where the V is) and the right extrusion length at the inside/top (where the V is) was pretty much identical.
After I shimmed (again with folded foil) both the extrusions (with the waste board on but not secured) I had to square the base with a little help from a strap that I secured diagonally.
When the base was squared I added the corrected X-axis extrusion (only the top wheels mounted to the plates) and checked for a gap. The gap is now 0.002mm at the front left side and 0.04mm at the back right side. It might be less after a machinist squares the extrusions but I think the numbers are just fine.
After this I mounted the motors and the bottom wheels and slowly tightened them until they where snug.
Now it’s time for the Z plate and then tramming I guess.
