Tec - there were lots of things in the end but here are a few major ones I remember:
Mormonism relies heavily upon the concept of a testimony, a personal experience with the divine normally expressed as a 'burning in the bosom' in the presence of 'truth'. Basically the slightly choked up feeling we get when we experience something very moving. I had a very exceptional experience has a young boy where after several nights of prayer about the Book of Mormons truthfulness I had a very strong emotional experience that seemed to fill me with love and - for want of a better word - bliss. This was a bedrock of my testimony. On my personal examination of my rationale for faith as an adult I decided to see if there were any circumstances where such feelings could be auto generated ( I had experienced similar feelings several times since while giving talks in church, bearing testimony as a missionary etc.) I read several books on how the mind works and on psychology and lo and behold I found descriptions of exactly what happens. The brain is a trainable and easily tricked organ that will engineer the reality you tell it to ( roughly!) and will throw in some surprise freebies ( a good example is color based optical illusions .) Continually seeking for an affirmative physiological response to a thought pattern ( prayer to confirm book of mormon true and by extension Mormon gods existence ) plus subjecting my body to unusual input stress stimuli that stimulate adrenaline amongst other chemicals (for example kneeling in a dark room / standing at a pulpit in front of people) and adding in an altered trancelike mind state ( hymns, prayer, language change - using thee and thou in prayer/ scripture etc.) all combine to be the perfect storm to engender and train the brain to produce otherworldy ecstatic feelings. Add this to a social environment where all respected authority figures and peers are coaching you and giving you an expectation of what you will feel it is absolutely feasible that you will have experiences over a lifetime which are mistakenly categorised as emanating from an external divine source. Young teenage me accepted those feelings as divine and thereafter every time I felt that sort of feeling whether it be at a good movie, at someone accepting baptism or an athlete overcoming challenges to win a race I re-ran the reinforcing meme in my head, ' wow I can feel the spirit of god, thank you for showing me truth .'
A huge one was evolution and the obvious falsity of a global flood ( Mormonism, unlike sophisticated modern Christianity of the last hundred years, absolutely requires a global flood as it is confirmed as such in the book of Mormon.)
Bible criticism ( Bart Ehrman's works amongst others) shattered both the old and new testaments. Coupled with Mormon prophets' fails ( I won't bother to list but there are some whoppers - see Hoffman and Kimball) allowed me to see every single prophet and their utterances as regularly incorrect / lies. This broke the idea that anyone - however lovely - was receiving divine information on my behalf.
Answers to prayer to which I could allude several allegorical personal and family examples could not withstand the confirmation bias test and more importantly moral test. On reflection very infrequently answered prayers were no different to fortuitous luck / self fulfilling prophecy ( please help me to control my anger leads to greater anger awareness ergo less outburst - damn it :) and importantly showed a petty god who answered my requests to get a job , find peace in my soul , have a good day etc while allowing my next door kid neighbour to be buggered every night by his violent paedophile father - note this is illustrative, my real next door neighbours were girls and both were raped by their father but not every night.)
In short my internal construction of Christ, heaven, angels, prayer, faith were all falsifiable and explainable once I accepted that my brain was a foolable organ that generated reality for me and then I allowed myself to really read evolution, biblical criticism, Mormon unvarnished history - all of which dismantled , with a wrecking ball, my faith. Brutally slaughtering my internal holy cows was painful but liberating. I held onto my imaginary but powerful world , despite all the very obvious contradictory evidence, way too long. My belief wasn't very strong when I finally really put it to the test.