Ok, all fixed and updated to the latest everything!
Moral of the story: Don't be a moron like me. I completely forgot that now, using Hekate, the Fusee.bin that I kept overwriting in the root directory is useless, and it needs to be overwritten in the payloads directory that Hekate uses for boot options. I think that's what Shadow#1 was referring to when he said update payloads, I just misunderstood it for 20 minutes.
Allow me to apologise now twice, once for taking up your time (and I really appreciate the speed of response and help on this forum) and two, to allow me to piggyback with a further question:
At this point it would be wise to backup the emummc, I believe, in the event such a thing happens again so that I can restore the current working state. However I was SURE I did that when I first set up Hekate, yet when I restored the eMMC from the backup (and it seemed to process fine) it didn't actually have any effect.
Correct me if I'm wrong: I just go into Hekate (at this point) go to tools and click 'backup eMMC' and that should be it? Then if it's accidentally updated in future I can just restore eMMC?
EDIT: Ok ignore this. I don't have enough space on my card to partition and backup at the moment, it's almost full. This is probably why the restore didn't work the last time.