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Sorry for the late response, I forgot about this for a while. I tried both ways you suggested, they both crash on booting the game. It's also not something I'd want anyway, since I want the games to be separate games from the official versions on my 3DS, not replacing them.
I found an issue playing the rom hack: while playing through the 3DS virtual console, you are unable to trade even if you applied a link trading patch. What happens is the game will not register an official Virtual Console release of GSC, and when trying to trade between 2 2.0 hacks, it...