Urs and Abraham,
First, thank you for the warm welcome :) I appreciate your speedy replies.
Full disclosure: I've only been using Lilypond for around three weeks. Long story short, I wanted to try and input / print out a copy of a Schenkerian analysis that I had done on manuscript decades ago, and decided to try and teach myself the language. What on earth could possibly go wrong?!
I unfortunately haven't created other files and so honestly don't know the source of the difficulties I'm having. However, the description that you provided, Urs, is exactly what I'm experiencing. It wouldn't surprise me if the issues are related to the \layout section and the values I've entered.
I'm happy to upload the PDF output as well as the source code - I just wanted to confirm that I wasn't breaking any rules before I did so. And if it's ok for me to go ahead and do that, please, be gentle :) It's definitely a work in progress.
Mike