Looks ok to me with that spindle mount position. One thing I did on my Mk3 was to drill and tap a second set of holes a bit higher on the Y plate so I had the option of mounting it higher for very tall work. Of course you can only reach across that work an amount until the Y plate may hit it but it is a quick feature to add at the build stage. I also added tapped holes along one edge of the Y plate to allow me to bolt a reference strip and maintain spindle tram alignment whilst adjusting the spindle holder. Never used it of course! But worth a mention

Can’t help on the ballscrew a that long and r&p as haven’t used them.

If you search the forum that sort of thing has been asked before and Jazzcnc has given advice