Don't worry, this is what I did all is fine.
Before anything, make a backup of your internal SD (just in case), EFS backup and all apps with Titanium. Then in Phils recovery select option to erase everything for new ROM flashing. I also did manual wipe of cache & dalvik just in case. Don't worry, your internal card won't be touched, but always better safe than sorry. Then flash MJ5 kernel, and finaly flash your chosen ROM. Then you can restore apps from titanium. I had like 2 apps that didn't work at all after restore, probably incompatible with 4.3. The system is stable 100%. Never had a reboot.