For someone who is a complete newb at trying to hack his 3DS, what are the steps I need to take to make this work? I get that I need the PSSE.exe and I put my 3DS's memory card into the computer, but what's the file directory to the Shuffle data?
Go to
http://smealum.github.io/3ds/, you'll see all the entrypoints that allow you to use homebrews on your 3ds. If your console is updated (aka firmware version 10.7), only the first 3 will work, so you'll need one of these games : cubic ninja, ocarina of time 3D or super mystery dungeon.
Read the instructions on the site. For cubic ninja, you can use the QR code level generator function to trigger the hax, for oot3d you'll need to inject a specific savefile (either from a pre-hacked 3ds or using the powersave), for mystery dungeon you'll also need to inject a specific savefile but it isn't possible to do so with a powersave yet.
Tell me if there's one solution you can use, you'll also need to download smea's starter kit and extract it at the root of your sd card (It contains the homebrew launcher and your first homebrews)
Once you have done this, you'll need to add an homebrew called svdt (it's a save manager). You'll find it here :
https://github.com/meladroit/svdt/releases , create a "svdt" folder in your SD/3ds folder (that you copied from the starter kit) and put 4 files in it : svdt.3dsx, svdt.smdh, svdt.xml & asr.dat.
Once you've done all of this, you can launch the HBL from your entrypoints, then launch svdt.
Select svdt & choose Pokemon shuffle with left/right arrows on the D-pad to launch it.
When prompted if you want to overwrite the secure values, press A. After that, your save will automatically be dumped in SD/svdt/Pokemon Shuffle/<date&time>, so you can quit with start immediately.
Now you can insert your SD into your computer (or use microsd management on a n3ds) and copy your savedata.bin on it. Use then PSSE to do whatever you want and save the edited SAVEDATA.bin, then put it back on your 3ds (wherever you want).
Launch svdt again. It's main screen is made of 2 columns in which you can navigate : on the left is the space reserved for your savefile, while on the right is your SD card content. You can press Y on a file to copy it to the current directory of the other column, so find your edited savedata.bin on the right & press Y to inject it into your save (press select when asked to overwrite).
Now you can launch your game and you should see your edited content in it.
Tell me if you're stuck somewhere, I'll try to explain it further !