1: Sounds like he meant you should delete game updates before first loading it off JB backups, perhaps? As there is no problems by loading saved game files in a game with JB'ing.
2: No BM is installed there untill you delete it. As for putting them on external HDD, that is possible if its FAT32, but compatibility from loading from external HDD varies. You can see a compatibility list at top of the page.
3: You can just install the fw over the cfw and it will be back to ofw, simple as that. There is already ways to get GT5 to play on JB 3.41 fw