I remember having a hard time getting everything straight as well, I think this is a side-effect of the printer design. It was hard to get the screws tightened down enough so that the makerslide would hold, but still be allowed to move to straighten corners and joints, and sometimes just tightening a screw was enough to ruin the alignment. I am glad I don't have to touch it anymore.
If you had a working printer, you could print a jig to help you build it square...
Cheers,
Ben.