-( Story related, cannot be missed )-
After defeating Lechku and Nechku in Kamui, all that really remains is to board the Ark of Yamato to defeat the ultimate evil that the previous enemies have all fled to. This is also known as the point of no return, as noted by Issun's departure. Be careful not to enter the Ark without either: a) an alternative save so you can go back to every area and finish up the other trophies up to this point, or b) fully understanding that, after you defeat the boss, you can start a New Game+ and go through the game a second time, possibly making some things easier on you. I'd really suggest just trying to get everything done before this point, so you won't have to worry about the second-playthrough (even though, if you completely obtained all of the Stray Beads, the Rosary received makes the second playthrough easier).
There are still some trophies you might not have by the time you board, being:
Everything else is obtainable by this point.