You don't need the "for" in your 3rd example: "How long has he lived here?".
Your questions are quite right. Yet, I'd use the -ing form with those verbs expressing an action that takes a long time to develop: "How long has he been living here?" "He's been living here for 5 years".
The point of a CCQ is to check whether learners have fully understood what they have just been exposed to. The idea is that they do know it - the CCQ serves to confirm this.
I disagree, I have tried many times without avail. i suppose you could ask at the end ....So ..... "how long has he lived there" emphasising that this is the structure.