Thanks for the reply.
I do realize that the resulting Jirachi will be no different then one I could inject manually with PKHeX. However it is the process that makes it feel more genuine and frankly, more fun.
I also did try to manually change the checksum with a hexeditor. I found the current checksum (3C71) at AFF0 and changed it to the desired one.
I then opened the savefile with PKHeX and re-saved over the old one. However, when I load this savefile up it sais it's corrupt and loads up the backup save instead.
Is there something I'm missing?