I'll answer as best I can.
1. I went with Rebug 4.30.2 spoofed to 4.41, I went with Rebug as it was the most recommended and they are always the first to come out with any updates if Sony update the OFW.
2. Not really sure, the Rebug I installed was CEX as standard.
3. There is no 100% safe way to making sure your not banned, but basic rules are never play COD Black Ops 2 online, never load up MultiMAN when signed in to PSN, or any other apps. You can still be banned at any time, I got banned just for updating my trophies, I never played online.
4. I never went into factory mode, just put the CFW on a memory stick and installed.
5. Yes you will still need MultiMAN or Iris to load up your games.