here´s a start:
in project > settings you can change
and other stuff
all can be saved as a .prefs file which can then be loaded at a later date
it sounds like you need to set up a cyc file to use as a template, with a customised layer structure, etc
i don´t think printer settings can be saved
only 8 pens in cycas 3.9
and i think the answer to most of your other questions is no, but they should be submitted to the wish list!