I have made progress with the error I posted, in case anyone was half looking at my problem...
I realised that the Nullpointer exception was because the Py.java class had a missing import and did therefore not compile correctly. I included two more external jar files in the Project's Java build path (constantine-0.4.jar and jruby.jar)
which seems to have solved most of the unexpected problems.
Running MainSep.java and MainOct.java now give the following error:
init: Bootstrap types weren't encountered in bootstrapping: [class org.python.core.PyType, class org.python.core.PyBuiltinCallable, class org.python.core.PyObject, class org.python.core.PyDataDescr]
Exception in thread "main"
A bit more of a 'contolled' error, but I do not know how to go about fixing it
Any advice much appreciated