Dead Space is fine, No AP25/26 Challenges, but Dark Souls is XGD3 and if you have the original you can use the official download of the new XBC and dae.bin file. Place dae.bin file in the same directory/folder as the XBC exe, and re-rip your game and you will be fine. you wont need to inject anything. Just re-rip your original.
As far as if you successfully flashed the drive. As always use the latest jungle flasher. Also your log will tell you if you have the loaded the 3.0. It does show as 2.0, but manually load the file for your drive.