While a little late on this thread.....I'm a big fan of "Big Z". To that end the approach our IronMan XE systems take to maximize "Z" is to, with dual X axis ball screws (optional or standard depending on system) allow the table surface the machine sits on act as the work surface. See picture for example of table we make to accomodate this and illustrate what I'm describing.
This adds either 6" or 8" (again, depending on system) of additional Z axis clearance inside the frame, without having to increase the height of the gantry risers....which we all know increases vibration/decreases rigidity and is to be avoid all costs.
Add to that our Z axis upgrade that has 12" travel and you have a extremely stable Z axis with over 12" clearance and the ability for reaching the entire 12" range with bits of your choice.
For more info check out..... Max Z Clearance