Movax has it right, why not just use a memory card if you are only moving game saves? They're relatively cheap.
As for FTP, well, easiest would be to use a gamesave exploit because you don't have to install anything on the drive. Just boot up the exploit, ftp what you want, and reboot the machine. That way it stays stock. Once you have the exploit booted you should backup your eeprom.bin just in case you ever need the hdd unlock code, like if you mess up while soft-modding it will save you from having to hotswap.