You don't have to get 100% completion to get this trophy, you only need to get 100% completion on the 13 Sequences that are story related. This means that you are not only aiming to complete the mission but to complete all the optional objectives as well. Most of the objectives are pretty simple, sometimes the hardest part is noticing objectives popping on-screen. To make sure you don't miss any I would recommend you press any time you enter a new stage of the mission to see if there any new objectives.
Do not worry if you miss some objectives though, every mission is repayable. Just keep in mind that you will have to complete the whole mission for the objective to count. If you leave a mission halfway through, the objectives you done on that playthrough will reset. Unlike previous games, objectives stack so if you complete an objective once you won't have to do it again on subsequent replays.
There are some missions that can cause a bit of trouble, especially the stealth missions and early naval missions where the Jackdaw isn't upgraded yet.
If you're having trouble getting 100% in a certain mission check IGN's100% Sync Guide or GameOxo Video Walkthrough.
Once you get 100% Synchronization in all Sequences the trophy should pop.