I'm considering the JMC 400W for one of my projects also.
Currently trying to figure out if it has 4000 counts per rev with quadrature on the 1000 line encoder. I suspect it might.
With a 10mm lead ballscrew, you are better off with a 2:1 belt driven gear reduction from the servo if you want to get the full potential out of it. Not saying it's necessary.
That's alot of stuff to read through, I probably missed most of what you said. And I don't know the answers to much of what you asked.
Check for the ballscrew critical speeds. How fast do you want to go?
There will be a bit of wiggle room in the free end bearing support for the ballscrew. This also allows it to move a bit from thermal expansion. So a machining error of 1mm shouldn't matter, it will be taken up by the free end.
About the bed....HDPE is a plastic...plastics can tend to expand alot with changes in temperature. What's the coefficient of thermal expansion on that specific one? Some of the van flooring I used to install would warp and buckle when parked in the sun due to this. The company making the floors switched to a material with a lower thermal expansion because of it.
The 3/4" plate for the table seems expensive....I would be tempted to say that with enough cross supports underneath, MDF would be fine for what you want to do.
One large power supply seems like a better choice to me. Not all of your motors are likely to be drawing over current at the same time.