Almost there: Z-Axis max travel settings?

I've changed to glass, using silicone to hold it in place, to offset my warped build plate. I've had to add a spacer as expected, on the Z-Axis, to stop the glass and extruder from colliding. I'm running into what I thought would be a simple issue to fix: After the print, the Z-Axis returns to the bottom and travels just barely too far. In doing this, it hits the bottom and upsets the bed leveling.
Is there a firmware (Sailfish) setting to stop this?
Or can I find it in Simplify3D?
I've gone through the onboard settings as much as I can, it doesn't seem to help. Simplify3D seems to have a max travel option, but I don't know how this deals with the print ending and the bed returning to the bottom of the printer.