Steve,
I believe that the majority of Y axis 'mechanical tuning' issues that people are experiencing are due to the inability of the end plates to align correctly and lack of some free play in the bearing rebates.
The above is more likely due to powder coating overfilling the holes and perhaps mounting screw hole positioning being slightly off. This will tighten the lead screws particularly at each end leaving no scope for the Y axis roller assemblies to align the lead screw as they move.
It seems counterintuitive but there needs to be some free play in the lead screw mechanism. Largely speaking the roller assemblies in the extrusions take care of alignment while the lead screws provide linear drive motion, not alignment primarily. This must be a characteristic of the lead nut/lead screw drive type and will be more of an issue the larger the machine.
My aluminum T slot bed is also a very precise fit and is likely constraining the available extrusion movement somewhat.
I have enlarged the size of the bearing rebates and the screw mounting holes with diamond files in both front and rear plates to avoid them misaligning the extrusions or applying stress to the lead screws when the mounting screws are tightened. Now both Y axis lead screws turn easily over the full range using fingertips only!
Once the customer accepts these slightly unpalatable facts, life gets much easier
Sadly most of us don't find out that there is a problem until the machine is fully assembled. By that time, it is relatively easy to remove the front plate but the rear plate involves more work.
Personally, I would have designed the end plates to interlock with the extrusions to remove the guesswork out of the macro alignment and designed in enough free play or adjustment range in the bearing rebates to allow some float in the lead screws.
Doug