After finishing my assemble and ready to hook up the electronics I noticed that the gantry was not square. I am starting with the default machine dimensions and when the gantry is at one end of the frame the sides are off by at least a few 1/10". Its not way, way off but its enough a quick glance suggest something isn’t quite right. The middle assemble printed great and everything fit together without really any extra effort (I did clean out the bolt holes with a 5/16" drill). Is there a solution to get thing nice a square? I am really surpised how far off it is based on how well everything fit together.
Triple check your frame. If that is nice and square and level my other suggestion is, I know it sucks, leave the center assembly on the rails, take out the 3"bolts, put it back together tightening all 4 a bit at a time. That will probably fix it.