First I would like to thank Vicious for an excellent build, and for helping out in this forum. My comments below are as much for getting help, as for helping improve the build. And if you need help from any of us with metric builds, let us know.
I have the same issues as described above with the 25mm build.
I currently have two suggestions I might try for aligning the center assembly.
One is making the holes in the image a little bigger. They are the only two holes that require force on order to make a fit. And forcing them into place, twists the assembly in the opposite direction of what I need. (01.jpg)
Second is filing down the part in the marked area, to allow the big X and Y parts to close in on each other, correcting the misalignment. (02.jpg)
(I also needed to drill out the 8mm holes)
I concur with the analyses, and I was about to do the filing myself..
But then I printed with 0.25mm layerheigh instead of 0.26 and everything fit much better.