Like I said in Part 1, I really liked Handley's discussion of revelation:
Revelation involves reasoning, but it is ultimately unpredictable and sometimes flies in the face of reason. That is not to say that it is unreasonable, of course, but in my experience it rarely matches our most rational expectations. While this can be challenging at times, if we think about it (rationally of course!), this is as it should be. If revelation always came in direct harmony with our expectations, then we could hardly call it revelation at all. It would be indistinguishable from the result of human deliberation and casting a vote. While such deliberation is essential to reaching greater understanding in a democratic society, in the church we seek revelation by combining the needs and thoughts of a group with our faith in a higher power. This does not mean we put reason aside but it does mean that we have to trust in a higher authority than in our own individual or even our collective wisdom.I agree that any meaningful understanding of revelation requires humility--the seeker/receiver by definition does not know the answer until revelation comes. It must at times differ from what we would otherwise do relying on our own wits. I think that's simple but profound, and needs to be kept in mind more often (speaking for myself, at least).
And I agree that if one believes the prophet is a prophet (and that being a prophet has some real, priesthood-y, revelatory meaning to it, however defined in the details), then you are under an obligation to seriously consider the things he says and give them a presumption of correctness. Automatically discounting anything they say that contradicts your priors means you don't really believe they're prophets.
However, by the same token, if you don't believe that leaders are infallible (which Mormons
Ultimately, I think if we're doing all this in good faith--being willing to humble ourselves to revelation that goes against our mortal preferences, but also being willing to seek personal revelation for church issues that trouble us--then we're a much stronger community. Disagreeing with a systematic problem in the church and trying to constructively and properly change it (however those terms are defined) is a Good Thing as far as I'm concerned. 
Consider the words of Dallin H. Oaks:
Revelations from God—the teachings and directions of the Spirit—are not constant. We believe in continuing revelation, not continuous revelation. We are often left to work out problems without the dictation or specific direction of the Spirit. That is part of the experience we must have in mortality. Fortunately, we are never out of our Savior’s sight, and if our judgment leads us to actions beyond the limits of what is permissible and if we are listening to the still, small voice, the Lord will restrain us by the promptings of his Spirit. I don't think it's outside the realm of possibility for someone to have felt that it would have been a good idea to call a person of color to the apostleship in this most recent conference--based on personal revelation--and yet to also believe that it was within "the limits of what is permissible" to call the three good, spiritual, capable men who were chosen.
In the end, I strongly believe that it would have been wonderful for the church to have a person of color (or two or three!) in the Quorum of the Twelve by now. I believe that it would be a blessing both substantively--race and ethnicity affect the way we experience life and thus how we experience revelation, so people of color would bring valuable insights to the table--and in the message we send to members and the world about truly valuing all of the diversity that God has created. So yes, I was disappointed that it didn't happen this time, and I do think we still have a systemic (not intentional or mean-spirited, but nonetheless serious) problem with race in the church. But I know we will get men of color in the Quorum of the Twelve, and I have faith that it will be soon. And in the meantime, I sustain Elders Rasband, Stevenson, and Renlund as inspired choices, and I know they will have wonderful things to teach us all.
 How to respond when you disagree with the prophet's/the church's stance on something is a whole separate issue. Clearly it could be the case that while not ideal, the stance is well within the bounds of moving in a general good direction, in which case there might not be any real productivity in disagreeing publicly (an example of this might be someone who disagreed with, say, the missionary age change--not a huge deal even if you think that 18 year olds are a bit too young to be regularly sent out to preach the word). On the other end of the spectrum (say with the priesthood/temple ban for blacks), it might be appropriate in certain situations to speak up and voice concern with the stance. The details of all that are pretty complicated and personal and I certainly don't have them figured out, and anyway they are beyond the scope of this humble blog post.
 See, e.g., birth control, evolution, blacks and the temple/priesthood, loving and accepting your LGBTQ family members, etc.
 Dallin H. Oaks, "Teaching and Learning by the Spirit," Mar. 1997 Ensign.