How would one go about squaring the gantry relative to the frame?
You first need to make sure that the cube/box frame is square. Once this is done, you need to check whether the gantry is still not perpendicular/parallel to the top frame. If not, you need to loosen the couplers at the front that control the Y movement of the printer. See if you can reposition the gantry to be square to the frame. If that doesn't work, you need to fiddle with the bolts that hold the wheels of the X-Y carriages so that the gantry will become aligned with the top of the frame.
Also would this account for the reason why when I attempt to print a circle it is not perfectly circular, and when I try to print a square, it is tilted?
Yes, a skew gantry causes skew prints, i.e. squares become parallelograms, and circles become oval. There is another solution to fix this in firmware, but, the preferred method is to mechanically fix the issue.