I'm going to elaborate on CroCop's instructions so I can explain it to the best of my ability to prevent any confusion on how to get extra jewels and coins in Pokémon Shuffle. If anyone still gets lost with my instructions, then let me know and I'll edit my post and try to fix it. For the sake of simplicity, I recommend you use HxD as your hex editing tool since that's what I used in my instructions, but it's entirely up to you.
1. Download HxD or another hex editing tool on your computer.
2. On your 3DS, open up SDF.
3. In SDF, look for the number 01410 under the User tab. Export the save data by pressing Y.
4. Now turn off your 3DS and hook the memory stick into your computer. The file you want is the savedata.bin, and you can find that at \filer\UserSaveData\201505XXXXXX\00001410\savedata.bin.
5. Copy savedata.bin onto your desktop or wherever you want, then open the savedata.bin with HxD
6a.
http://imgur.com/kGViGhg
6b. In the picture above, you'll see two boxes; a red and black one. In the red box, you need to change that number to 128 so you can find appropriate byte to edit, so change it so you can find the 6A byte.
6c. The value of the offset you want to edit is 00000000x6A, so you want the 00000000 row and the 6A in the column. You can look at the picture and look for the black box, if you need help looking for it. Once you find it, change that value to FF. Now save and exit.
7. Copy and paste your edited savedata.bin back to your memory stick in \filer\UserSaveData\201505XXXXXX\00001410\savedata.bin, then put your memory stick back into your 3DS and start up SDF again.
8. In SDF, go to the SD tab, and there should be the user data with the number 00001410. Import that data by pressing A.
9. After you import the save data, you have to go back to the User tab and look for 01410 again. You need to delete the secure value by pressing R+X so you can use your save file.
10. Start up the game. You should have 15 jewels, and you can get 99999 coins when you spend some coins or even simply start a battle, I believe. Enjoy!