It has been brought to my attention that you may be confused between the KFU (Kindle Fire Utility) and TWRP (Team Win Recovery Project). The KFU is a Windows based utility used to change bootmodes, install custom versions of the recovery and bootloader partition images along with various other tasks. It has no affiliation with TWRP, COTR, or FireFireFire, other than it installs them to your device for you.
However, the "bug" in TWRP mentioned earlier is due to that way it handles the updater scripts in certain ROMS. It has nothing to do with your system files. The reason you have no system files right now, is because you wiped them prior to attempting to flash a ROM. Since the ROM was never successfully flashed, you have no system files in place, therefore nothing to boot to.
Downgrade your version of TWRP, or install a different recovery altogether, make sure you have wiped data (factory reset) and reinstall your ROM. After that, you should no longer have any problems.
I strongly suggest you take the time to read the guides and tutorials available for the Kindle Fire and make sure you understand how everything works before you do something and get yourself in a situation that you can't get out of on your own.