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Hi Emily,

here are the answers, probably not satisfactory:

  1. To further work with the prefix as a net you shoudl use
    the mci2ll tool found in pep/bin. This reads a prefix and
    generates a PEP low level net. If you just want to apply
    some tools, this should suffice. If you also want to view
    the net, you should try the -L option to mci2ll, which also
    generates some graphics information (not really nice layout,
    though).

  2. Unfortunately, I did not manage to find enough time to
    start on this. It is on my schedule for some years now, but
    I have no ideas yet when it will finish.
    There is, however, the possibility to simulate
    counterexamples with time. So if you checked properties on
    time nets, your counterexamples may contain the special
    transition "tic" and the system bell will beep for each time
    step during the execution.