Um you have it backwards adding the rom and putting in the ID by using CTRL+ALT+E screws up the sfrom, its better to add the sfrom directly to hakchi
In Hakchi CE maybe, but not in Hakchi2 (still on 2.21f version). Haven't used CE, so I don't know how it works. (I'm talking specifically about the IDs here. I know hakchi2 doesn't build 'perfect' roms.)
There's no point in building a rom with SFROM Tool when you are testing these patches. Just patch the game with LunarIPS, drop in whatever hakchi you use, add the ID and test. SFROM Tool is to build 'perfect' roms as Nintendo themselves would have made them for the VC. For the purpose of testing, you just need a vanilla clean rom.
But anyways, if doing it that way has worked fine for everyone so far, then carry on. However, when test-patching, if you encounter some strange non-reported behavior, try patching a clean vanilla rom and adding it directly to hakchi just in case.