Design looks good. Are you looking to get more travel than your present cnc mill with the same performance? I'd also advise making some denim bellows for the linear slides. Really helped mine with the swarf. Did you ever look at a 1.5kw Chinese spindle with VFD option. For what you're doing might be worth the investment.
You sanded both surfaces perpendicular by hand
? You have a bigger pair than I do.