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There are some, uh, minor text issues, but otherwise I got it to work and send to a Japanese Game!
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For those curious, the PokeCardeE Disassembly only alters one of the region checks when you set it to compile to Japanese, there's three. In a decompiled VPK it's 44E, 465, and 467h, change them all to a 1. Kind of a note for myself but yeah that'll do it.