Thanks for sharing the screenshots @Adam_Hillier ! Very helpful and I see the problem. Krona is looking for a count value in the first column, then categories in the others. Your file is missing that first value.
This is the Help from the tool form (scroll down to find this, plus links to the original tool author documentation, any GTN tutorials that tool is included in, plus sometimes topic at this forum).
Krona text input requires a tab-delimited file with first column being a count, and the rest representing the hierarchy
Then, for a full Metagenomics pipeline, we had a topic recently where I broke down where to access resources like use guides, tutorials, and workflows with that context. I think this will address the other parts of your larger questions. → Kraken2 reference database for shotgun sequencing data - #4 by jennaj
Hope this helps! 