You didn't merge the old updates with the new. Any title that has not been updated after 9.2 will not show up if you do not install the old updates. Follow the instructions below to solve this and your keyboard issue. I am not a fan of the guide in the op, too many people are having the same issue with the keyboard.
1. Get all of the updates for the system region you want to switch to starting from the lowest you can find (4.2) to whatever your emunand is now (9.2). If you are using a N3DS get the O3DS updates up to 8.1 and then get the N3DS updates from 9.0 and up.
2. Merge all of the update cia's into a single folder overwriting older versions with newer versions (add 4.2 cia's to the folder then 4.5 cia's then 5.0 etc..) when you are done there should be around 170 files.
3. Delete all cia's starting with 0004001B, 0004800F, 00048005, 00040130, 00040138, and 00048005. These will prevent the emunand from loading.
4. Place all of these cia's in a folder named updates on the root of your sd card.
5. Use FBI to uninstall the main system titles from your emunand (system settings, mii maker, miiverse, camera, etc...). If you region change before deleting the system titles it will cause your emunand to freeze randomly and block you from entering the system settings app. (Compare the system titles of the region you are on with the region you are going to on 3dbrew.org. Delete system title with unique id's that do not match.)
6. Use sysupdater in emunand to install all of the cia's in your update folder. When this is done your system will reset.
7. Use decrypt9 or rxtools to inject the SecureInfo_A for your new region into emunand. My system was weird in that I had a SecureInfo_B instead of A so rxtools would not work but decrypt9 did.
8. Congrats!! You have a region changed system. Now format it and update however you like. I updated with a cart to 9.4U first and then updated through system settings to 10.4U.
The eshop will not work unless you had a SecureInfo_A from a system that never connected to the internet.