1) If I flash the AP, CP and CSC files will I achieve 100% stock with bloatware?*
Yes this adds it all back.
2) Will this return my "add call button"?
3) Is it as simple as just using odin 3.09 and flashing* the AP, CP, and CSC files?
Yes, be sure to put the phone into Download mode first then open Odin, Then attach you phone via the USB cable that came with your phone.
4) I also understand that this will take me back to* G900AUCU1ANCE but will I be able to do an OTA do go to G900AUCU2AND3?
Yes your OTA update to AND3 will be available.
5) Is there anything else I need to know to prevent my phone from bricking!
This will not brick your phone. DO NOT DISCONNECT THE PHONE UTIL ODIN SAYS PASS!! Flashing all three will erase your personal settings and wipe the phone like a factory reset so back up your apps to your Google account and your contact to the SIM card or Google account.
If you did not trip KNOX when you rooted, using Odin will not trip it either. When in Download mode, your KNOX indicator will be shown at the top.