Finally found a way to make 4.3 roms work on my phone, here's what I did, starting from a bootlooping 4.3 rom.
Restored stock 4.1.2 using Matt's utility
Rooted with Matt's utility
Put 4.3 rom and GAPPS on external SD
Fastboot flash CWM 6.0.3.5 (or install via Matt's utility if you like)
Wipe data/factory reset
Wipe Cache/Dalvik
Go to mounts/storage and format /data and /data/media (/sdcard) **Back up anything in your internal SD you want to keep before doing this!**
Flash 4.3 rom (I used PAC nightly 9/26)
Wipe Cache/dalvik
Flash GAPPS
Wipe Cache/dalvik
Boot up and setup rom
Reboot
The 2nd boot went very fast for me. I think the key lies in formatting /data and /data/media through the CWM mounts and storage menu (or /sdcard on other recoveries) before you install the rom.
Hope this helps!