Tried to get the campaign working using the older rules.csv from the last Ironclads version. The big thing is that you absolutely will want a jar to make this work, and you need to provide a modified rules.csv. Stripping down the Ironclads rules.csv or copying from it is probably the best place to start.
Notably, there is no setStartingRep function to be used by the rules to set up your rep with each starting faction, there is no payFee to be used for requisitioning, etc.
I'm sure there are plenty of other things missing still. I can try adding the stuff in bit by bit when I can find the time.
As Okim says, an IDE would be very helpful in figuring out how to code the Java portions. Kazi has a good guide on setting it up for modding Starsector:
http://fractalsoftworks.com/forum/index.php?topic=10057.0