I'm stupid close to an S rank in Just Cause 2, due to being able to listen to other things while playing. I've finished the game and all my meters were maxed before I did the last agency mission, but I only have 47 out of 49 faction missions. I can't find them anywhere! Are there two 'secret' faction missions? Can they open up in Mercenary mode or am I screwed? WHERE ARE THEY!!! ARRGGGG!!!!!

Try filtering, you can make what icons appear so just make it that only the faction mission icons appear, do you have any strongholds left to take over? they open up new missions

Yeah just filter (LT or L2 -> press hide all -> press faction missions) and look closely. Roaches missions are harder to see because they're light blue and all.