A couple of questions about root and OTA

I have been on stock almost all my life, but I once thought what could go wrong with having a rooted phone. I unlocked the bootloader, and tried just booting a custom recovery TWRP, and it worked, although it didn't work before as I heard HTC disabled booting recoveries only. Flashed SuperSU, and VOILA!

I installed a couple of applications I wanted to try, first of them was Titanium Backup, and removed a couple of applications like the default "Internet" browser. I also installed greenify and played with it for while.

Yesterday, I tried installing the latest OTA that fixes the Stagefright exploit, and my phone got soft bricked stuck at the booting screen. Thanks to a Nandroid backup I made with TWRP before rooting - or even after rooting I really can't remember -, which I restored, got the OTA normally but wiped my phone.

Here are my questions:
- Does root only change system files?
- If I removed the default "Internets application that came with the phone after root "uninstalled" it, does this change stock?
- Would greenify with root cause that?
- Is there any official way to restore the stock system files?

I'm just trying to figure out the exact reason here..