Well, I used Misumi extrusions (link in the BOM), which are custom cut to your custom requirements, so all the extrusions will be fitted at their end points. Additionally, the 3D printed parts (frame brackets and gantry brackets) help square the corners. A bracket is fitted on the top/bottom and all 4 sides of the frame.
I built the frame in 2 pieces and married them together. The instructions show this process. Since all the X/Y-axis extrusions fit together at the end of all Z-axis extrusions, the process of squaring things up is just a matter of using the brackets to hold the pieces together. The gantry brackets further enforce the frame is squared up for the gantry.
After the frame is all bolted together, the rest of the assembly is practically the same as the UM2. It was insanely easy and it was dead-on accurate right out of the gate. The only thing I needed to spend time on was getting the steps right for the extruder. I was using a 1.8 degree steps and running 1.75mm filament, so I printed a calibration piece on the UM2 and dialed on the new printer until they looked the same.
At this point, I can swap the SD card from machine to machine and get identical results.