For me it was making peace with the fact that the Church was run by men who are just as flawed and sinful as I am.
We all want to be forgiven and to be cut a break when we screw-up. Well, if we want to receive that, we have to be willing to extend that as well.
Granted this can be difficult when you get a bunch of arrogant, haughty men in red hats stomping around and claiming to be infallible.
No organization run by men, including churches, will ever be flawless. You could leave for some other denomination but there you will just find a different set of shortcomings. The good things about the Church far outweigh the bad IMO. Jesus directly told Peter he would be his rock, and that mission is one worth sticking around for.
You were forgiven. And cut a break 2000 years ago. When Christ died for those "screw-ups". It is His FINISHED WORK for you that ensures you are "cut a break".
And you're right, no organization run by men, including churches, will ever be flawless. Only God is flawless. Which is why we can never be saved outside His own perfect flawlessness. And even more incredible is the fact that He DESIRES to be reconciled to us. He reached out to us. 2 Cor. 5:14-21. Instead of writing mankind off as hopeless, He reached down and saved us from ourselves. He gives us a new life, a new identity, and a new purpose: ambassadors for Him. To proclaim His mercy and grace to those who have not met Him face to face. But there is only one way to be reconciled: the finished work of Christ. Not my demand. God's demand. And I thank God every day for His demand, for there is no other way I could ever please Him and His flawlessness.
And I look to Peter when I feel I’m too flawed. look at his doubts, his sometime arguments, and still Jesus told him to be the leader, knowing that Peter’s faith would overcome all of those human frailties. And I know that I am too forgiven and loved by Jesus.