I read this through. The current pop-up menus are a dead-end. Sorry for the hard words. Well - usage for a beta-game is ok, but for a release I think they should be replaced by another interface.
Some issues I had with them: It's definitely unfair, when you start as beginner and open the inventory, doing search and then the creepers come. I lost my life some times in the beginning with that.
Then I mixed up many times producing an item with having an item. Because the left an right side looks not very differently. Call me stupid.
Suggestion:
I think this: A menu on the left/right of the screen could work. The left menu-bar is for the inventory/build and the right for research and tech-tree.
By default, the left side (inventory) is shown with icons, as far, as there is space on screen. This means for example, that it shows only one stack per item, and/or it shows the most used items first. When hovering, the inventory pops out and shows the current inventory. I would add here all the "hidden" inventory stuff, like ammo, guns, fast-access-bar etc. because I searched some minutes for a steam-engine after production, until I saw, that it was added in the fast-access.
For production there is on the top an icon (or press E as currently). This opens a list of items, sortable/filterable by category and other searchable criteria and displays the current total number of items you have in the inventory in small letters besides the icon. Hovering like now: You see, what's missing to produce it.
The right side looks not much differently. It shows the current research in progress (much smaller, than currently), and it lists all currently researchable items, so with one click you can research it. Simple.
Opening the research shows the research-tree. This is a list of researchable stuff, sortable/filterable. You can set a "target", one item, you want to get to. All items, you need to achive that are for example blue now. So when you close the window you only have to look for the blue icons and click them to start research. When there are no blue icons left, you have researched your target.
In every case, when opening any window, it tries not to be placed above the player in the middle and is a little bit transparent, so you might see creepers but in every case, the view to the player should not be covered with anything.
PS: This is also true when opening chests and all other items: It's really not good to place a window over the player.
PPS: Is this a bug? Open chest and walk, walk, walk. The chest keeps open. Should be closed when reaching the limit.