You will find the Dromons your largest problem. I once chased one for about 20 years; this was with massive naval superiority too.

Seems you do not have 2+ ships per sea region so must be early in the game; dedicate at least 3 provinces to building ships with production staggered; this way you get one ship per turn and avoid the cash crunch of trying to build them all at once. As said earlier, attack! attack! attack! Once a faction starts a naval war I rarely let up until every ship is sunk.

The Pope?
His influence can be lessened somewhat by using assassins. When playing a Christian faction, I always have one province pumping out assassins for this reason; once you have all the assassins you think you need use the same province to produce spies.

Have fun