Regarding the final boss, there's an easy way through and a harder way. For the harder path, you've already discovered that Lucas's Chakram one-shots the blue barrier. For the red, Emily's charged red bow will destroy it in two shots, or four uncharged shots. When he teleports around, he's easiest to hit with her. For the yellow barrier with Caelan, it's a bit tougher, but it's easiest to hit him by jumping over him when he dives at you and using your wind blades to hit the barrier from above. When he lands, shred him by jumping with Lucas's red sword and attacking.
Alternatively, when he lands and pulls out his large sword, you could try grabbing it from him. With Caelan, if you have the dash wing, shooting yourself upwards with wind blades makes getting it trivial. With Emily, you'll have to wall jump to reach it. That should make things significantly easier.
Regarding the item above the first save point, a character you meet in the post-game will tell you how you can access that.
