The Y axis rods seem to be a bit too long for the overall case size; they stuck out the better part of 2 mm.
I applied a 3/8-inch Forstner bit to the inside of the rod end caps to make a slightly-too-deep recess, then shimmed the hole with some cardboard to make the answer come out right.
The Z axis rods were just barely too long, but I did the same thing to those caps.
The X axis rods were fine!
The Smell of Molten Projects in the Morning 