EmperorBrandon said:
One thing is what to do with ぢ and づ - they make more sense as "ji" and "zu" in my opinion since that is closest to how they're pronounced. I've seen things tagged differently on Danbooru, such as with the main character of Tonagura being "Arisaka Kadzuki". Is it OK to change these?
Most definitely yes. "dzi"/"di" and "dzu"/"du" are another example of random inconsistent conventions that have very little to do with the actual state of things, this time in the name of consistency with how you write kana. Modified hepburn explicitly assigns them "ji" and "zu", the same as with じ and ず, as that's their phonetic value. If you see them, either change them or report for a mass edit if they're big enough.