Hello again . Seems a bit quite around these parts, where's everyone gone?

Anyway, it's been a while (cough, 10 years) but I've finally got around to starting to build this CNC. I started by building a sturdy bench for it to sit on. I was on safe ground here. The cross members are 2x9's and it's covered with a sheet of 18mm ply.
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I made my first mistake while making one of the support brackets for the x-axis box section. I was rushing and I managed to break a drill bit. In the replacement hole I then managed to break a tap.
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Moving swiftly on... Here's a shot of all the parts I've put together so far carefully arranged to make it look like I've done more than I have. I was going to mount the linear rail to the box section when it occurred to me that might not be a good idea. Obviously, I've got to get the x-axis exactly perpendicular to the y-axis. I feels like I should build the y-axis and mount it before drilling the mounting holes for the x-axis. Does that sound about right or should I mount the x-axis rails now and then try to adjust them square to the y-axis later? To adjustment them I'll have a tiny bit of play in the rail mounting screws or I can get more by opening up the holes that mount the x-axis rail assembly to the frame. It feels like I'll only get one shot at this so I don't want to screw it up.
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