1. Here is Okuma dedicated chat. Sure, it's better to ask there.
2. Can You please be more specific what is the problem with Z axis limits?
3. If I recall correctly, if You command on the soft limits "ADD 0" <return> you will get the selected soft limit = system limit.
4. The difference:
Machine limits = expressed in encoder units directly, you see there some crazy numbers like over 15m written in microns.
System limits = deending where the system "0" ( = origin ) is set these figures gives understanding where is what. These limits are adjusted to hardware limit switches, means absolutelly inaccessible for user.
User limits also controled by variables are limits adjusted to specific work set.
Protection limits ( collission avoidance, also controled by variables ) are set specifically for the work setup and prevent collission.
If he tool offsets are described correctly, the collission avoidance prevents tool - chuck, tool - other turret, tool - steady rest, tool - tailstock collissions.
And the last one. What do you mean saying "pulse motors"?
And what relation can be between motor design ( or any other harware piece ) and use of imperial / metric system?
This is a calculation inside CPU only and nothing else.
By the way, Okuma does really good transition between the measurement systems. You can use both on every segment of shape.