There is a story in the Book of Mormon called Lehi's dream, or Lehi's vision (1 Nephi 8). In this dream, Lehi sees a straight and narrow path leading to the tree of life. To get to the tree, the crowds of people must cling to the iron rod and follow it to the tree. In the distance is a "great and spacious building" filled with people mocking those who go to the tree, but those holding steadfastly to the rod ignore the mockery and push forward.
“For strait is the gate, and narrow the way that leadeth unto the exaltation and continuation of the lives, and few there be that find it.” -D&C 132:22 (see also Matt. 7:13–14)
"Hold to the Rod,the Iron Rod,'Tis strong and bright and true" -Hymn #274
This story was always encouraging to me. I looked to the commandments as a constant source of guidance. The teachings of the church were my rock, my firm foundation, my iron rod. It didn't matter if "the world" mocked me for being Mormon. I wouldn't drink coffee, I wouldn't swear, I wouldn't listen to "bad" music, I wouldn't watch "bad" movies, I wouldn't skip church, the list goes on and on.
I was going to cling to the iron rod until I made it to the tree of life.
But at this point in my life, the summer after my junior year of college, I had several items weighing on my shelf of doubts. How could I know which the teachings of the church were "doctrine" if prophets and leaders sometimes "speak as men"? How could I trust an organization that withholds some parts of their history and doesn't publish their finances?
I still wanted to have faith in the scriptures and doctrines of the church, so I looked to church approved sources for answers. My patriarchal blessing said that I should: "Read, study, and ponder the scriptures, and the prophets that have lived since the prophet Joseph Smith."
I understood this to mean that I should study church history, so that's where I started. I took a church history class at BYU called "Global Church 1900-Present" and used that as a baseline for my own research. I didn't like what I found, which was that the history I knew had been more white-washed than I realized. The thing that bothered me most was that the Mormon version of history always stressed "inspiration" and "the will of the Lord" while never admitting the reality of certain circumstances.
To explain what I mean, I've thought of four big issues that stand out in my memory. I've broken them down between the Mormon version of how the issues have been handled and the reality of the circumstances that existed in the larger context outside of Mormonism.
Mormon version: Ask any Mormon missionary or member of the Mormon church and they will tell you no, the church does not teach the practice of polygamy. Polygamy was practiced in the past, they'll admit, but it was ended in 1890 because of the will of God. They will call it an "inspired revelation" or use a similar phrase to expresses the idea that God alone was the catalyst for this change.
Reality: The Edmunds-Tucker Act was passed in 1887. The act made polygamy illegal and would cause the church to lose all of its assets to the US government unless they disavowed the practice.  The church's response from 1890 is known in Mormon scripture as Official Declaration 1, which proclaims the end of polygamous teachings in the church (though the church didn't quite get rid of all polygamy in their doctrine. See D&C 132).
The prophet at the time admitted that the decision was not made entirely based on God's will:
"On September 25, 1890, President Woodruff wrote in his journal that he was “under the necessity of acting for the Temporal Salvation of the Church.” He stated, “After Praying to the Lord & feeling inspired by his spirit I have issued … [a] Proclamation.”" 
The phrase "Temporal Salvation" = $$$$. The threat of losing real estate was the spark that "inspired" the prophet to make this proclamation. Mormon's don't talk about that part, though. They focus on the part that says this revelation came from God. Whether intentional or not, they white-wash the history by not discussing the Edmunds Act because it was a major part of the context in which the church made its decision to disavow polygamy.
Mormon version: The inspired revelation from God known as Official Declaration 2 cleared up previous racism and ended the priesthood ban that was keeping black people from entering the temple. Church leaders spent many hours in the temple "supplicating the Lord for divine guidance" before receiving the revelation to end the ban in 1978.  The leaders were truly inspired.
Reality: The 1960s Civil Rights movement, which happened years before Official Declaration 2, was the real catalyst for clearing up the racism of the church's priesthood ban, not a revelation from the Mormon church. Again, the Mormon version omits the critical context of the progress made by the Civil Rights movement and white-washes the history in a way that emphasizes the revelatory inspiration of Official Declaration 2 and dismisses the impact of the work done by Civil Rights activists like Rosa Parks, Martin Luther King, Jr., and many others to raise awareness of racism in the United States. Without the work of these activists, who knows when (or if) the priesthood ban would have been lifted.
Temple Ordinance Changes
Mormon version: I grew up being taught that the temple ceremony is a sacred revelation from God and that God never changes. It was more than a little shocking when I first learned that the ceremonies have changed over time. To be honest, I don't actually know how most Mormons explain the changes because they hardly ever talk about temple ceremonies in general. One clever way to talk about the changes is to avoid the subject entirely:
"What has changed in the temple ceremony? It’s probably more important to understand what has not changed." 
Reality: The symbol of slashing your own throat was removed from the temple ceremony. You are also no longer required to be naked under a poncho during the washing and anointing, a ceremony which included being touched on various body parts by a temple worker. First of all, eww. Second, HOW COULD IT NOT BE CHANGED?? Being touched by a stranger while you sit naked under a poncho or making the gesture of slicing your own neck open is really creepy in any context, and especially creepy in the context of a religious ceremony. It seems obvious that the church would have to remove those parts of the ceremony if they expected people to enjoy going to the temple.
Like I said, Mormons just don't talk about the temple ceremony. They will say that Joseph Smith received the ceremony through "inspiration" and talk about how special their experience there is, but then they will say that the rest is sacred, which basically means they want to keep it a secret. The pervasive white-washing of temple issues and why God changed his mind about the creepy parts of the temple ceremony is really tied up in this sacred secrecy, which deserves a post of its own.
Women Praying in General Conference
Mormon version: General Conference of April 2013 was the first time women were allowed to pray during the sessions. God loves His daughters and treats them as equals with His sons, so of course, women should be allowed to pray in church meetings. One women's response to this historic event was: "I am so full of joy and love for a Heavenly Father that answers prayers and inspires change." 
Reality: The part the Mormon version doesn't acknowledge is that maybe it wasn't God who inspired this change. The reality is that women's rights activists in the church had been working on issues like this for years, and in the time shortly before this conference their activism had been gaining momentum. I remember getting my own invitation to a "Wear Pants to Church" Facebook event in early 2013, and it wasn't long after this conference that the Ordain Women movement began staging protests. It wasn't allowing women to pray that caused these movements. These movements had already been at work for years. Reaching the milestone of women praying in General Conference, followed by other big events that followed, were the results of their efforts, not the cause.
The idea that activism or politics could change the way the church operated had never been a part of my worldview before. It didn't seem possible that the will of God could be influenced by political and social pressure, but it looks like it has been.
The more I learned about the actual history of the church, the more discrepancies I saw between the faith-promoting narrative of the church and the reality that the church responded to these situations in a way that any organization would: they caved when the pressure became too much. None of these instances showed foresight or prophesy. It was all reactionary, not inspired.
I came to a conclusion: the "iron rod" of church doctrine zigs and zags as often as it needs in order to protect the organization, and the God of the Mormon church seems to change his mind a lot. I didn't feel like I could trust the church's "inspired revelations," or any of their "doctrine" for that matter, to keep me on the straight and narrow anymore.
My shelf was reaching a breaking point.