How far off is it, 3/8″ across the diagonal? they should be bolted down as perfect as you can get them, withing a 1/16″ should be easy enough? If the gantry bars are off when you put them into the rollers they should get closer as they force them more square.
You should be making any adjustments with the z axis in place, or at least the rails, they open it up. You can follow the new instructions it is pretty similar to the old one. So I suggest making the outer frame as square as possible, with nothing on it. Then make the center assembly as square as possible with all 4 rails in place but not on the frame, then when you connect the 2 it should actually get a little better because of the rollers trying to align things.
If it is really far off check the calibration of your printer, all three axis test a 100mm movement with calipers it should easily be within about .2-.5mm over 100mm.