So, it turns out that whilst booted into Aroma with the two USB sticks in, I can't actually get any data from the USB stick with the majority of my Wii U save data and I can't get update data either.
Mario Kart 8 is the only one that actually worked completely since I had my data on console (I only have an 8GB model) and I was able to play online (and win a race

). Text and Miis don't display correctly though and I don't know why.
Tried seeing if I could get update and save data over, but the only way to do that is to disable Aroma (by holding R when booting) and launching Dumpling from a web browser. It kept crashing a certain amount through a dump and it just meant I wasn't able to dump anything other than some small digital games (Art of Balance and NES Remix 2) and some save data.
Not sure where to go from here honestly. The guide at
https://cemu.cfw.guide could really do with more information, it was relatively easy setting up things like Pretendo or vWii stuff but it isn't with dumping Wii U titles.