Blackhawk,
It sounds like you must have an older PRT with normally open switches for X and Y on Input #3, set to Normally Open Limit (VN). Your Z switch should also be on #3 if it is indeed the same as the others (Normally Open). Do not change Input #4, as that is your E-stop and should be set as a stop, either normally open or closed depending on your switch type. If it doesn't work, I'd check that you do have the same type of switch on the Z. Also check that it trips on the target, you may need to adjust it closer.
If you are using an older SB3 version, you may not see the "Has Z prox" option and the needed code will not be in your homing file routine.
Edit, I see that your tag line states that you have a PRT Alpha, but it must have the older NO proxes.