Long story short, when I started looking at church history, and compared it with the beliefs of the modern churches, I realised the gulf between my evangelicalism and historic churches. The main difference for me was the sacraments, and understanding and experiencing how they are so much more than just symbols. It took a while for me to decide between RC and EO, but on 3 issues I realised I just didn't believe the RC claim. The first was papal authority. Another was the filioque, where it's clear cut historically that the western church added to the Creed, and the 3rd was the Immaculate Conception. I have been greatly blessed by many RC authors, but in the end I couldn't become Catholic in good conscience, whereas I found no such problems in Orthodoxy.
(For the record, I'm still not officially Orthodox, but only because I am waiting for my wife to view Orthodoxy more favourably.)
May I also offer one tip, while you struggle with these doubts? Keep reminding yourself of the things that you do know, that are not up for discussion. Christ was incarnate of the Virgin Mary, died for our salvation, and rose again. You have been united with Him in baptism, and these doubts you are experiencing don't change that at all.