Use a savegame manager like Checkpoint to backup all your saves. System transfer will get all your legit games on your new 3DS, you'll have to manually reinstall any pirated games (not that you have any of those
). Then restore your saves.
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Also, I would highly recommend making sure your hax are up-to-date on the old 3DS first. Make sure you're using the latest versions of Boot9Strap and Luma, that way you don't have to worry if you need to run system update before you can system transfer. I'd recommend also setting up DSiWareHax beforehand, it may cost you the price of a cheap DSi game from the eShop but that way you won't need a flashcart to install hax on your new 3DS.