Saying Parshas Haazinu is a Segula for Emuna. So is Sippurei Tzaddikim. Get more, and deeper, into Torah and Mitzvos. Daven to Hashem for more Emuna.
Speak openly to Hashem; tell Him that you will remain loyal even with all the questions you may have. This is very powerful and can break through barriers of Emuna.
There is no Mitzva to entertain every opposite-of-Emuna thought.