Hello! Thank you for bringing this to us, we'll be happy to go over his powers with you at a later date. For the most part, power nerfing on missions is subject to the mission, so checking with us like this is exactly the right way to go about it. 😊

As for your questions:

1) Amaterasu will indeed be able to burn pulsefire. Only one weapon at a time, though, so Itachi can't use it to burn all the used pulsefire at the same time.
2) Susano'o will be able to protect against it, but the more pulsefire attacks it is subjected to, the more it will start to weaken it — so eventually the pulsefire would burn through it. We'll leave it to your discretion to decide how many attacks it takes.
3) Genjutsu does work on some of them, while some seem immune to any mind-related magic.