Thanks for the suggestions.

For the gantry, i'm going to have it stress relieved and then milled back. For the frame, i'm going to use an epoxy bed - i think that getting the frame milled flat would be very, very expensive.
I'll add some diagonal bracing to the frame too.

As for the ballscrews, I think you're right Jonathan - the critical speed for this design in a 16mm ballscrew would be around 1600rpm. That's probably near the limit of what the steppers can provide.
I will thicken the plate used for the Z axis - I would rather not reverse the rails and blocks.