Found one of the causes of the excess power consumption; the ADC. It seems to get the greatest benefits form sleep mode, you need to explicitly disable the ADC before sleep and (if needed) re-enable it on wake. This does not get disabled with the other on-chip peripherals. Anyway, I've committed the change to the repo (https://github.com/LinusDilon/Insulin-Minder). After a week running with the change the battery has dropped maybe half way. I think I'll get at least two weeks, and maybe as much as four out of it now.
An another note, I'm starting to look at whats needed to builds one from scratch using a custom PCB.