You can easily check if root was installed properly by running an application that requires root: root explorer, titanium backup, etc...
FFF and TWRP definitely failed to install. wget also failed to fetch the files in the first place. Can you tell us a bit more about the way you're using KFU? Did you try placing it in a short path, such as C:\KFU ? Are you right clicking and "Running as Administrator"? (this can mess up the paths) Did you edit any of the files? Take a look in files/files.log as well... OR make sure KFU/wget isn't being blocked by a firewall of some sort.
You may want to just redownload KFU and start from scratch. Also, double check the drivers, even if they appear to be working right, make sure they show up like in the table here: http://xdaforums.com/showpost.php?p=23747671&postcount=2
Thanks for the suggestions. I tried moving it to a short path and temporarily disabling firewall before running root installer again, but it doesn't seem to be working after I tried running setCPU. Driver seems to be installed fine as well. I'll try redownloading and see if that fixes anything.
EDIT: Whenever I ran the batch file, even though I didn't right click run as administrator, it would say administrator in the title bar. I tried running it when logged in as a standard user, and the word is gone from the title bar, but the results are the same. I haven't edited any files, and this is what my files.log looks like:
updateurl|http://kindle-fire-updates.s3.amazonaws.com/update-kindle-6.3.1_D01E_4107720.bin
updatemd5|2754961C4DC2C0F37BE7B7D1206C57FF
twrpurl|http://goo.im/devs/OpenRecovery/blaze/openrecovery-twrp-blaze-2.1.1.img
twrpmd5|2F10DFB3575C08E789745B4E883B4C55
cwmurl|http://icxperia.com/doomlord/kindle-fire/KINDLE-FIRE-UtterChaos-CWM5-touch-v01-FINAL-1_recovery.img
cwmmd5|980F152121AFD5DCD12B732669E21B09
appsurl|http://random.kennocha.com/kindle/apps/apps.zip
appsmd5|B694AC497F4AB9FFC62F124B738D9112
fffurl|http://random.kennocha.com/kindle/firefirefire/fff-u-boot_v1.4a.bin
fffmd5|D6A85FFE24EC48C132665E8D6852BF3E
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