Church/Mormon history is kinda my thing. I've literally taken every class offered on Mormonism's history at BYU -- both in the Religion Department and History Department -- and I'm currently TA-ing the premier Mormon history course offered at BYU. I also do significant research for my professor, have helped him on the Joseph Smith Papers project, and have written several papers on Mormon history that have received significant praise. I'm currently working on a submission to the Mormon History Association. In short, I know what I'm talking about, and not just because I've taken Susan Easton Black's class, served a mission, and dabble in Mormon books because it's interesting. It's because Mormon history is LITERALLY my life. Okay, so I haven't read Wilford Woodruff's complete diary, but I have used it as a significant source in several papers, and I have handled and transcribed previously unpublished primary documents relating to Mormon history. (It was legit, by the way.)
So I figured I'd offer my two cents on the matter to the person who asked this question; I know a comment would probably be rejected because the "writers already adequately answered the question." Fair enough, I'm not a writer, and the answers were adequate to what the asker probably wanted. Buuuut this is kinda my pet subject, so here goes
Gimgimno
First, I COMPLETELY agree that Sunday School isn't the place for talking about the warts in our history. Do I think that the CES should do a better job of covering them? Of course, but CES is a bureaucracy that has its own agenda (which it likes to pass off as God's Pure Truth, but I won't get into that here). But Sunday services are for building faith, not academic exploration. Sometimes when I'm teaching I use some of my history background to contextualize a quote or story in a way that the manual writers would probably hate, but real discussion of the historiography of the Utah War is completely unnecessary in a lesson on how God sustains his people during trials.
I disagreed with Gimgimno's recommendation that the asker go to the FAIR wiki. Sure, it's useful, but it comes across with a sort of pleading and defensiveness that is really unnecessary. Most Mormon scholars wouldn't be caught dead there. Richard Bushman himself, who gave a speech at their annual conference a few years ago, told them how much he hated apologetics. To their faces! At their annual conference! And this is from dear, faithful Brother Bushman who is one of the gentlest, kindest men you will ever meet.
Rough Stone Rolling is a bit dense. It has great stuff in it, but Bushman isn't the strongest writer in the world. It's tough to get through, and that's coming from the kid who has read piles and piles of books and articles on the subject. His scholarship is amazing! But if the question asker wants a brief introduction to these sorts of issues, I wouldn't recommend it. If Bushman is really what you want, go with A Very Brief Introduction: Mormonism. It's a quick, light, easy read that covers the Church pretty fairly and skims the surface of controversial issues (Book of Abraham, polygamy, Mountain Meadows, etc) engagingly. It also has a recommended reading list at the back.
P.D. Kirke
I think that the recommendation of The Mormon Experience was spot on. That's the book used as an introductory text in BYU's history department (where they teach REAL history), and it's completely fantastic. Arrington and Bitton really did a good job on it.
However, I would recommend The Story of the Latter-day Saints instead. It was written for people exactly like the person who asked the question: faithful members who want an introduction into real history, not the stuff of CES. It was quashed by Elder Benson because he thought it didn't portray the leaders in the best light; for instance, it talks about the Word of Wisdom in context of the times, especially the temperance movements of the era. (For instance, did you know that the Kirtland Distillery was purchased and shut down TWO WEEKS before the Word of Wisdom was given? And that it was shut down by members of the Kirtland Temperance Society, which included members with the last names Lyman, Morley, and Coe? Yeah... tell me that Joseph wasn't influenced by that when he asked God about alcohol and tobacco. Puh-lease. Anyway, the origins of the "Emma was sick of scrubbing tobacco" story are spurious in my opinion.) Anyway, The Story of the Latter-day Saints is written to explain the history as history to Mormons of a faithful background.
I thought the recommendation of American Moses was random, though. Arrington's stuff isn't really the most up to date, and his contribution to the historiography is important, but not the best thing ever. And Brigham Young? Random.
To the Question Asker
If you really want to go down this road, your testimony will be necessarily shattered. The things in Church history you learned in seminary, institute, at BYU, and in Sunday School are incomplete. Once you get exposure to a more accurate representation of what really happened, what you think about the Gospel, the Church, and its early and present leaders will change. You will feel like your house is being swept off the sand, and that is exactly what is happening.
However, once that happens you will able to choose to rebuild on the Rock Himself -- Jesus Christ. Many don't do that, become cynical, and throw the baby out with the bathwater. They might stay engaged in the Church for cultural and social reasons, but they don't engage themselves in the Gospel of Jesus Christ. There is a difference. You will have to choose. You will have to be okay with the fact that men are fallible, and that includes the prophets. But you will also have to be okay with the fact that God chooses fallible men to do His work, and that you must sustain them anyway.
So let your testimony be shattered. Question what you thought you knew. But then have the humility to let God take those pieces and build them into something stronger, and do the maintenance needed to keep it that way. I promise it's worth it.