Case 1. Bob is the leader.
Case 2. The leader is Bob.

Both of the above could be changed to the same interrogative sentence "Who is the leader?" where in case 1 the subject ("Bob") is replaced with "Who" and in case 2 the complement ("Bob") is replaced.

My question is about when they are further changed to indirect questions.

Case A1. Who do you think is the leader? ... Bob is.
Case A2. Who do you think the leader is? ... It's (The leader is) Bob.

Case B1. Do you know who is the leader?
Case B2. Do you know who the leader is?

Are they all gramatically correct or could one or more of them be wrong or otherwise unnatural?

Thanks in advance.
All are common. B1 is sometimes challenged, but I shan't.
B1 strikes me as less natural than the others, but I have no solid reason to claim that it is ungrammatical. The others are all correct and natural.