MPQ doesn't ask for root access so there is a small chance it is the main culprit. It couldn't access system files. Most probably it is just a coincidence.
Do you have custom recovery installed? Flashing stock images via recovery or using adb/fastboot might help.
My HTC Desire Z was once in similar state, reflashing stock images was the only thing that worked.
You can always try ROM from http://www.cyanogenmod.org/ If you never tried it it is like stock+fixes+ some additional useful settings
I know that stock should be the best one but in Android quite often it isn't. (for me it was like: HTC stock for my Desire Z = battery life is horrible, stock for Nexus 4 = phone getting hot, colours little off, Sony Xperia J = with stock forget about multi tasking)