Default [Q] Phone unstable after rooting

So I have a Galaxy S2 that was rock solid stable. It would always reboot without a problem.
I needed to root the phone to get an app to work so I installed TWRP backed up phone and rooted the phone. Found out the hard way not to grant SU to any app as the phone went crazy deleting processes and killed itself.

I restored to pre-root system rooted again and only give SU to the app that started the need - BubbleUPnP.

No other app is granted SU priviledge. BTW this might be noted in a sticky or put in a rooting thread.

However, phone works fine but at least once a week it hangs on a boot. Never gets by the Samsung loading screen. In fact the working bar is almost at 100percent and it freezes.

I have to pull battery and restore a TWRP backup. This is turning into a hassle.

A prior thread said to do a factory restore. If I do that will TWRP be gone and my backups? Other thread said do something with Odin.

Is my Android os - jellybean - not stable for rooting and rooted apps like BubbleUPnP and exposed framework? If so what ROM Android os build would be best?