I just add a solution adding some info for those still going for this game achievement.
1) You need to have ALL collectibles (Quantum Ripples, Intel, Chronon, Documents, Computer and Media) You can see that in the menu. Follow this guy playlist with all location (and by time in the timeline : https://www.youtube.com/playlist?list=PLuGZAFj5iqHcuxKo2sML1...
2) If you change Junction (for unlocking other achievement for example), some collectibles (the one that change depending on the choice you made) will be reset. So you will have to find them again in their modified version. BUT
if you change the junction back to the Timeline where you already find the collectible, it will still be collected. So you can change junction, but be sure to come back to the one you collected everything.
3) If you are stuck at 96%, you MUST
play again the last level, and at the moment you unfreeze Will (after killing Serene) the achievement will unlock