What I do is go into twrp's wipe menu:
1. Factory Reset wipe x3
2. Cache wipe x3
3. Dalvik wipe x3
3. System wipe x3
4. Flash in rom + gapps, boot up, wait few minutes to settle in
5. Reboot recovery, flash in tibu, boot up
6. Restore apps, sms mms, reboot
Then I'll adjust my regular settings, jb control center settings, trickster mod settings, softkeys. Then i use Nova pro to restore my beautiful widgets, hd widgets, play music etc..