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You downloaded the .zip from the forum with the two .ups files in it, right? Now you need a vanilla pokemon emerald rom and some program to apply the ups patch to it. I used NUPS.
What an amazing and huge hack this is, it really is baffling the amount of work put into this. I mainly wanted to congratulate you.
Secondly, I noticed that in shiny Passimian's sprite there's a lot more blue than there should be