Rubacava is 1 THOUSAND km from El Marrow, that's a lot, specially in a hostile world full of dangers and monsters like the one of the game. Also El Marrow is huge, probably Hector and his men don't have a reason to think Manny would just leave the city instead of hiding there. Salvador tells you right at his last letter that rumor has spread on the streets of El Marrow that Manny fled to Rubacava, so seems clear that they didn't find out he was there until almost a year has passed.
Regarding your doubts about year 3 events... It's all pretty straightfoward and explained in the game, seems like you didn't pay attention or don't remember the events clearly.