I use machine coords for my safe Z and usually set it at zero or close to it, maybe -5mm.
The limits are likely correct, it will just depends on what you have set up, X is M2, Y M2, Z M3 so it doesnt really matter that you are seeing + on some and - on others.
Softlimits would normally be set as X and Y min and Z max as Zero X and Y Max would be the travel of each axis so in your example above 50 and 100. Z Min is the travel of the Z in a negative value.
If you home to the fully positive ends of your travel put a Home Off value equal to the distance the axis is away from the fully negative travel.
Abnormal condition LEDs are a PITA, its a warning telling you somethingis not what you normally have, it may well still be correct so click on the LED and see what it says, if you think its correct tell Mach it is by double clicking on it and saying OK to reset.
Hood