After receiving wind that I may have overdone it on the complexity, I've just uploaded a manual explaining some of the more confusing aspects of the game. Hopefully this should make it a bit easier to understand :).
I've also uploaded a new version, labelled as post deadline. This version is in all cases identical to the deadline version, it just has a few changes around the place to make some things more intuitive. For instance, the starting help screen is no longer the hardest enemy in the game.
If you've been putting this one off because of its intimidating complexity, or tried it but given up in frustration, feel free to come back and check it out again, now that it actually makes some sense.