Thanks a lot for playing and glad you have fun with it^^
The powerful Item can be found near the Labatory where you get the Manticore TF. There is another hidden entrance nearby where you need a certains forms ability, and since you have all you should have no problem getting it. Also great job at finding all three of them!
1. That is a very tricky one. You most likely have the key already if you opened most of the chests in the snow forest area. For a hint: You might want to check your weapons ; )
2. The one on the northern plains is just another way to open the way to the final dungeon. So if you already opened the way through some other route it does nothing anymore. Just one more possible way to reach the ending.
As for the Shrine one: It was supposed to let some extra Mythical Flames appear but now that I look at the code I think I made a oversight and they do not appear. Will fix that in the next bug fix update, thanks^^