You pretty much explained your problem in the first part of your post. Pretty much all issues you have are related to the 'Time Skip Phase' you have yet to unlock. The 'Time Skip Phase' is the next part of the story after the final battle against Raziel. It continues to explain the events in the world on a special map that is sorted in acts that are in a chronological order. By continuing the main story, you'll learn about it and be able to unlock the things you're missing, including events to upgrade the classes of main party members that increase their max level to 200.
Since the time skip phase is still not completely done, it's possible to go back and forth within the acts and also to the phase before the time skip content, so you can freely advance to it and try out things without having to worry.