Here are some alignment tools I just designed and printed for when I install the new carriage on my Eustathios. The vertical-alignment/squaring/paralleling of the components is the trickiest part if you ask me. Hopefully this can help others, and I am hoping they help me as well.
STL files are here: https://drive.google.com/folderview?id=0B1rU7sHY9d8qVnp2WWxxZTFCNVU&usp=sharing
The large red and blue parts are for setting the rods at consistent heights at the corners, the smaller bars are for setting the cross bars parallel to the side rods when tightening on the pulleys after you tension the drive belts.
I modeled the corner levelers around the components from my solidworks assembly. So I can only guarantee they should work for the files out on my github. I included bolt holes that may help hold things even more ridged during assembly. Lets hope they work.