I've made something usable
I realised that I don't really need to create an index in the MOBI file as the Kindle does a search on the full text that is fast and easy to access, so I made a very simple HTML file and converted it to MOBI using Calibre, which I only had to modify very slightly to stop it converting all the GIFs into JPEGs. It's rough, but it's usable.
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