Hello, I'm (marginally) back for the time being. I see my "perfect" patch wasn't perfect after all but this within itself is a misdemeanor because nothing programmers ever come out with is truly perfect, EVERYTHING will always have bugs, even the more professional of applications.
But enough about that, let's work on the responses.
This is exactly what I did so I think the most I did for you was save you about 5-ish hours of work and thorough testing. From what I've seen and played, the Japanese revision of the code that adds the system is indeed well put together, as none of the bugs posted in this thread are apparent in the Japanese ROM, which leads me to believe that more then just the registry values and memory positions are different between the hard coded mechanics of the US and the JP ROMs.
The "Minus" bug truly baffles me; I can't think of a reason why it would do this. If the Plus ability isn't bugged but Minus is, then my patch might have altered the position of Minus' code, which is causing the game to crash because the pointer to Minus' code is now incorrect. I'm not sure how this could actually be possible though, so don't quote me on this. It still confuses me.
Flash Fire, however, I can explain. Flash Fire's code references the edited part of the mechanics as part of bypassing the damage. Flash Fire is meant to make the Pokemon immune to Fire moves, so in order to do this, it references the damage dealing code; which this patch edits. Fixing Flash Fire means changing the address that Flash Fire's code references so that it can properly bypass defense. It's relatively easy to do so long as you know where Flash Fire's code is; I don't know it personally however. Once you know, it's just a matter of comparing an unpatched ROM to the patched one and finding the values that Flash Fire's code references.
no$gba has far from perfect emulation. From what I remember, the version of touhoumon that I grabbed this code from doesn't work in no$gba either. Suffice it to say, you sacrifice some compatibility in using this patch. If you had the debugger version of no$gba though, with some ASM knowledge, it's quite possible to make a patch that is compatible with it.
The Japanese continue to impress me. I was never aware there were DPSS versions of Touhoumon Emerald. Unless Putin wants to give a whack at it this time, I could very well cross compare both those patches and make a DPSS patch for Emerald. It'll likely contain the same bugs, or possibly new ones, however, which is a job for a good ASM hacker. I'm merely here for the boring jobs no one else wants to do. ;o