Re: Z axis noise - what kind of axis drives do you have?
Re: Z travels - Did Z home normally, all the way up?
Go to MDI and command a G32 move, this should take Z to toolchange position. Take the air off the machine and pust the toolchanger arm in. Does the height look right?
If not, go check the PPU values in the parameter table.
If so, go check the travel limits in the parameter table.