I can understand saying "I was wondering how is A doing?" is not grammatically correct. Instead we should say "I was wondering how A is doing?".
On the other hand, I was wondering which one or both is grammatically correct:
- "I was wondering what are the differences between A and B?"
- "I was wondering what the differences between A and B are?"
In my opinion both are correct, and the first one seems more balanced the the second, as A and B can be long.