Wishmaker Jirachi is generated by checksum. This was specifically done to prevent SR. So if the Jirachi is not shiny, then reset, play the game in some way, save, and try again. If someone has made documentation on how to RNG this by manipulating the checksum then go for it, otherwise its basically a shot in the dark.
You could play the game and contribute zero to the checksum because fun fact, the checksum calc was broken and instead of considering all checksums, if uses one from a specific section based on order of the save parts. And I don't see an easy or possible way to identify your save section order without save editors.