I'd think using the tools from Fanoush's initfs_flasher would work fine... I'd copy initfs_flash, and make a modded version that doesn't start with the current initfs, but with the image, and then does the same stuff; while it's stopped waiting for input, you can muck around in the initrd directory, and then it'll jffs2 it back up and flash it. Am I missing something? Is the initrd in a different format not readily extractable to a raw fs image?