What is the status of those three Sahaba- in particular the 1st who was referred to in the verse 9:40, and the 2nd who ruled after him? Did the Prophet not know of their tendency and desire to take the Khilafa from Imam Ali or was Allah alluding to these two in 9:101? Why did the Prophet bother to spend as much time among them as he did?

This is a major objection that I've heard- that if they weren't good people, why did the Prophet spend so much time around them and marrying their daughters?

The prophet (s) was sent to all of mankind, not just the good natured people.

We can see the status of the oppressors in the Quran where Allah curses the Zalimeen. Now what about those who oppressed His beloved prophets family?

The prophet married many different women due to political reasons which can be found in the books of history.