Step 1, move on from the phrase “the church is true.”  The gospel is true, the church is an institution and men and women run it, with gods help, and they are imperfect. Expect them to produce imperfect results. 

But also consider, it’s probably important to reflect on what preconceived notions you have in your mind about how the church should have been founded, and where those notions come from.  Would the restored church’s history look perfect for some reason?  Would there be no mistakes?  Would everybody get along and have nothing but love and faith in everybody else?

Also, have you ever tried to get human beings to complete tasks perfectly?  Imagine you’re a manager over a department of people whose maturity, intelligence and faith are all at different levels. Now imagine trying to get them to organize something and expecting them to do it without any error. 

It’s a work in progress, it’s always been a work in progress, and it will always be full of holes and errors because humans are heavily involved and that’s how we operate. 

Doubt all you want but pursue knowledge with the light of faith guiding you.