As he planekrazie’s said “The way I got everything square during the welding process of the frame was:
1: Find you a good FLAT surface.
2: Get a scrap sheet of steel. I used the surface of the steel workbench which is 4×8.

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3: Lay the legs and table support ( one side at a time ) and get your measurements. After you have everything set in place, Get some small scrap steel chuncks or steel rods and spot weld to the surface of the workbench in all critical corners of your frame. Its just a plain jig. This keeps the frame of the machine square when welding. Only weld small beads at first. Go corner to corner then middle. Check to make sure it is still the way you want it. Then make your finnish weld. After welded pick it up out of your jig and lay the next side in place. Do the same steps as the 1st and wala Identical sides. If you look at my frame, The side legs and top where the rails mount and the lower mount for the table surface is the 1st side. Weld it up then go to the next side the same way. Adding the front supports that connect the 2 sides together is easy. Make your measurements use a good set of clamps and just make a spot weld until you are satified with the squareness.
After I finnished with the middle supports I took a measurement from front right corner of the frame to the lower left and vice a versa. Same way I do when I build my rc planes when I align the wings. I am only a amature my self. The last cnc I built was pretty good. You can see it in my members photo section.
Guys have a good weekend. It might be sunday before I can mount the y axis to the bearings. I have to go back to the slave pit this saturday.