So, to recap:
1. Install, make sure Henkaku is working. Launch MolecularShell (MS).
2. Start an FTP server with MS and connect to it with your PC. I recommend using Filezilla with
these settings.
3. Dump/Download your app.db [ur0:shell/db/app.db] Since you've got your FTP server open, now is also a good time to download the folder for MolecularShell to your computer. You'll need this for a later step, so let's just do it now to save time. This is located in "ux0:/app/MLCL00001".
4. Open app.db with a SQL editor. It's recommended to use SQLiteBrowser. Open up "table_uri".
5. From here, you want to create a new record with properties (NPXS10000;1;ux0
if you're using a PS Vita or (NPXS10072;1;ux0
if you're using a PSTV.
6. Additionally, if you're trying to dump the game from the cart, you'll need to create an additional record: (NPXS10000;1;gro0
or NPXS10072;1;gro0
for the PS Vita and PSTV respectively.
7. Open up the table "tbl_appinfo". From here, you want to search for the ID of NPXS10000 or NPXS10072 (depending on your model), and filter the val field with "eboot". Change the data in this field to "vs0:app/NPXS10027/eboot.bin" and make sure you save your changes to your app.db.
8. After this you'll need to upload your fixed app.db back to your PS Vita with MS via FTP. Reboot your system, and reinstall Henkaku.
9. After Henkaku is reinstalled and working, open up the Browser on the PS Vita and in the URL bar you're going to want to type "ux0:app/APPID" (if the game is digital) or "gro0:app/APPID" (if using a cart). If you don't know the App ID, you can get it from the box of the game if you have a cart (or from the cart itself), the PSN store, or just Google it. The US version of P4G for instance is PCSE00120.
10. This will open up the manual for the game if you've done everything correctly so far. Now you'll want to minimize this (you'll notice that your game's manual is contained within the LiveArea for either Email or Near).
11. Open up MolecularShell and re-open your FTP server. Navigate to "ux0:\Patch\" and either create a directory for your game "APPID" or delete/backup the contents of the existing folder. In P4G's case this is going to be "ux0:\Patch\PCSE00120" for instance. Upload the contents of the folder from MolecularShell into this directory.
12. Once that's complete, close MolecularShell - start the game itself, and it should instead boot up MS. That's because in Step 10 you've replaced the executable for the game in the Patch directory making the Vita start Molecular Shell instead of the game itself. Re-open up your FTP server. Using Filezilla, navigate to "/App0:". This will show you the contents of your game, regardless of whether it's digital or physical. Download this folder to your computer to complete your dump of the game.
13. Once your dump is complete, you'll want to delete the MS files or restore your old patch data for the game you just dumped so you can actually play the game again. From here on out, you should be able to just repeat Steps 9-12 to dump any additional games as long as your app.db has not been modified again.