You will need to have a flat surface to mount your rails on, you will not have a flat enough surface from the square tube, especially after welding. you may want to look into that. Your Y axis should be ok if you get some nice flat plate, the X will probably be off a bit. Maybe you could shim up the low spots.
Also, I would probably add an additional leg in the center of the long span. You dont want that to sag, although its probably strong enough.
And I'd still try to redesign the Y/Z carriage, I dont like how the Z hangs out like that, have you looked into moving the Y rails to the backside and building a box around the Y beams? or even mounting your Y rails on the top and bottom of the Y beams. Either one could bring that spindle in closer. just my opinion.
Looks great though, it should turn out pretty solid.