Not remembering what I have to collect next brought me to using a notepad. I think an in-game version of that would not just address the problem of not knowing what to collect but that in return would also lessen the problem of a cluttered storage, like you described. Maybe pinnable recipes that track what you already have (inventory and storage) or literally just an in-game version of the windows notepad, so that you don't have to tab out every time to look at it. Of course you already can look the recepies up in the utility section of your pouch but that's even more cumbersome than doing what I did, especially if you are using it repeatedly.
That would be too invasive/handholdy for me. An in-game notepad could be easily justified as something you carry with you and it would be useless without your input. Maybe there is another way, this was just the solution to both of these problems for me (with additional application as a general note keeping device).