I originally never tested v1.1 on real hardware. All work was done using Citra and it's cheat feature, along with Cheat Engine. The offsets for both the original and the v1.1 rom were identical. If the codes for the original worked on real hardware, and both rom versions used the same offsets in Citra, testing both seemed redundant. I'm not sure why the offsets are shifted on a real 3ds for v1.1. Most codes work by adding 0x1000, but there are some odd ones like 0x001BFF80 (v1.0) is supposed to be 0x001BFD78 (v1.1 Citra), but on the actual 3ds it's shifted by 0x200 to 0x001BFF78.
It'd be nice to know what causes this, but it seems to be working now. I've updated the original post with the new build.
Thanks, I checked the codes I planned on using and they all seem to be working well except a few small things:
Moon Jump: makes the game unstable, it crashes randomly on day and area changes. if you're writing it as a word value (gateshark 0x0 command) this is probably why, it is a short (gateshark 0x1 command). I tested both word and short using the fort 42 code and both work but word causes random crashes as described so if you plan on looking into this look there first.
Change Day: day 1 and 2 turn off and on in a radio button like way but 3 and 4 don't turn off/on at all (trivial as the codes all appear to work as intended but this may confuse some people)