Crazy About Mini's - For the arm stop, that is the procedure I have done, so that should be set correctly. For the Throw Out Nuts, that is also what I have done, although the plunger ran out of threat when I was winding the nuts in while the pedal was pressed, it did end up flush to the casing and I could turn it a bit more after the pedal was released, but not a full flat.
Something is not right there. Never ever known one run out of threads. You can normally see the treads before it is depressed.
sounds like everything is worn and you are also not getting 1/2” of travel at the slave.
try re bleeding the system.