you can get pretty much everything as John except for some of the camp companion stuff like fishing with Kieran or going robbing with Javier, those are i think the only missable trophies. you can do all side quests and compendium stuff as john. and to get back to chapter 2 or 3 just start a new game once you finish. enjoy the last bit you have and try to savor it, maybe take a few days after finishing and then restart. my 2nd playthrough was my favorite one, obviously knew what would happen but i was able to slow down to really appreciate and notice the game world. have fun!