[8.9" Kindle Fire HD Q&A, Help & Troubleshooting] stunts513:
OK I'm burning this app with fire for deleting a very lengthy tutorial I just wrote and somehow deleted by bumping spacebar... Lemme edit this post from my laptop where I don't have to worry about apps that screw me over.

You will understand why i am really po'd right now after i finish retyping this message again and see how long of a message i typed that got erased in an instant :)

Ok so what i'm going to tell you to do involves your own kindle that your got back up and running, you need to dump the emmc from it which in itself is not completly possible unless its hooked up to your pc via a sdcard reader to the motherboard like before, but in this instance you don't really need to because if i remember correctly i can still fix it if the dump is complete enough. This would be easier if otg was working because you could dump to a flash drive but thats still not working just yet so no worries. What you will need to do is boot into twrp and go to mount and uncheck everything except data, then it connect to a pc and run these commands:

adb shell dd if=/dev/block/mmcblk0 of=/sdcard/emmc.img
adb pull /sdcard/emmc.img .
adb shell rm /sdcard/emmc.img

This will take quite awhile to dump and pull as it is going to be a huge file, i recommend clearing as much space off the kindle before you do this as you can(atleast 2gb). Now let me explain why this is not the best idea to do normally, first off this is going to result in an incomplete dump as we are going to be attempting to dump the entire emmc (which is like what, 14 gb it think?) and dumping it to the same storage device that already has space used on it, so theres no way it could fit, so it will just error out at some point, but by the time it errors out it should have finished the important partitions, the biggest partition is the last partition if i remember correctly, which is /data. The other reason this would be a bad idea is because we are trying to clone a entire drive/partition and when doing that you would want all drives/partitions to be unmounted, but since we have to store it on the emmc we have to leave /data mounted in order to store the file. It isnt a good idea to generate an image of a partition while the data is being accessed and modified, but in this case twrp is barebones compared to android so not too much in data should be in use and the data partition is going to be incomplete/corrupt anyways when we get this working.

Now once that has finished pulling and you deleted the file on the device itself so you won't have literally no space left on the device, try running this with the other kindle hooked up via the sdcard reader and all of its partition unmounted:

sudo dd if=emmc.img of=/dev/sdb

i believe this is the correct command, it might need a bs=1 added to it but i'm not positive, i don't deal with flashing kindles emmc's personally, i just can take educated guesses at the command paramters because of linux experience. Now when it is complete i recommend ejecting the kindles sdcard reader and plugging it back in and seeing if gparted will show you the correct partition layout, at which point i'm guessing it will either say the last partition on the list is either unknown, unallocated space, or might even say ext4 but it will more than likely be corrupt. The best news about this is that if you already have twrp + second bootloader on your kindle, then when you turn this kindle on it should be able to boot into twrp and you will more than likely have to if the /data partition is corrupted. Once in there i'm not sure if a internal storage wipe will fix the problem or not, you might have to manually run a command via adb shell that reformated the partition but i'm not positive. So when you get it as far as the partition showing back up please post back and i can provide more instructions.

^^Now you see why i was so po'd since i origanally typed all this on a touchscreen...