This is what worked for me
I am happy to report absolutely zero issues on my S4 installing and using Super S4. Let me detail what I did, and maybe you can go back to square one and start over with better results. Prior to installing SS4 I had the OTA version 4.4.2 with NAE modem.
1) After reading through the Super dev thread, I decided to use Philz recovery. I downloaded this one: philz_touch_6.23.9-jflte.tar.md5 and flashed it with Odin 3.07. I made sure to disable the auto reboot, as that has caused trouble for me in the past.
2) I downloaded 1.4 odexed and copied the file to my ext sd card. Then I checked the Md5 sum of the file on the card.
3). Booted to recovery, used the "Wipe Data/Factory Reset>-Clean to Install a new ROM" feature. Twice.
4) Under "Advanced" wiped Dalvik, twice also.
5) Rebooted recovery. DON'T FORGET THIS!
6) Flashed the ROM zip.
7) After flash, Selected "no" instead of "disable install recovery"
Everything came up beautifully. Be careful which KTweaker profiles you use, I had weird stuff happening with the "battery saver" profile. I am using Ktoonsified V6 now and battery life is great.
Hope this helps!