Making a ROM hack isn't that easy. First off, you need to so some web searching and find a program that can actually extract the source code, art and music files, and other assets from the ROM file. From what I know, even once you have the program it can be a difficult process. Second, you have to actually know how to program in whatever language the extracted source code is in. Creating events (like your Jirachi fight) and doing pretty much anything other than sprite or sound edits requires programming knowledge. If you're not a well versed in some version of C coding (which is probably what the game was written in), I recommend you just give up now.
As for editing art like the sprites and title screen, once you've extracted the art files any half decent image editor will work. Photoshop is the best, but even MS Paint works ok if you know what you're doing.
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