For people trying to rebuild CIA and are getting the makerom error, download the most recent version of makerom from github and replace the one in the folder. it fixed my problem. seems like the issue is that the makerom exe provided straight up is broken.
Unfortunately I think the tools are broken. It said it was able to rebuild the files into a cia file, but all it did was create CustomRomFS.bin, which is completely unusable for me since I barely understand this stuff at all.
I don't know why this stuff is so complicated. I just wanted to play a randomized ultra sun game but the stupid randomizer saves it as a cxi file instead of a 3ds or cia file.