I finally got it working! It was my dump- I instead decrypted the catridge from godmod9 instead of dumping or using anything else. Then I used ctrtool to extract it into romfs and exe folders. I knew as soon as I loaded it into pk3DS I had done something right- the exe was editable! Turns out the Youtube tutorial was correct, just a slightly different dumping method was required to make it work properly. Maybe it is different for US/UM but I'll be using this method from now on regardless. So I now have fully randomized X and Y versions up and running, and the technique down! Not to mention I increased shiny rate to 30% for fun and have been having some amazing encounters lol.
Now that I know how to do it... I'm gonna one day build the impossible game that's incredibly hard to beat lol.