I need some assistance!!

I just finished completing all botw and I recently just started playing totk... and my problem is that I'm halfwayish through the game and I don't have everything I need for the Pura Pad or anything else?!

I have the master sword, I have all the geoglyphs, and I'm defeating all the problems in the four regions, but I feel like I'm missing things like why there is a Phantom Ganon under the great Deku tree, and a lot of stuff to my knowledge in the game is blank.

I feel like in botw you get told everything to do and you do perfectly fine throughout the game!!! Is this a me problem, or is this a totk problem?