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I've been wanting to do the same thing - tried just patching the code.bin with LIPS but it immediately crashes Citra upon attempting to run the game. Same thing happens with Prismatic Moon. If it's not too much trouble, would you mind uploading the code.bin for Eternal X/Prismatic Moon?
Out of curiosity, are the Mart item changes present in the Rebalanced and Legal versions? I've got Insanity X and Rebalanced Y and in X I have both pricing and item changes (e.g. $40 Cherish Balls instead of $200 Pokeballs) but in Y I only see pricing changes ($40 Pokeballs instead of $200...
Here you go: jmp(.)sh/vOdOPLC (sorry, can't post links yet so just remove the brackets)
I actually built a v1.4 CIA of Eternal X a few days ago with 5.3, it worked fine for me. Are you getting the error of it not being able to find 3DS Builder? Because if so you have to run SetupUS.exe and...