I think that the CNCRouterParts.com Z axis works much better when the carriages are mounted back to back instead of on the Z plate that you have in your current design. I originally made my Z axis that way and had the same concerns that you have about travel and placing the cutter too far from the bottom bearing.
CNCRouterParts.com also sells what they call their "high Z plate" that allows for what I believe is a much better back to back mounting of the carriages. I made my own plate because I wanted to incorporate a spacer needed for my design. Here's a link for their plate: CNCRouterParts and a photo: