1) Not really sure on this.
2) There are Backpack mods (I'm currently trying out "AdventureBackpacks" for the first time and like it a lot, highly configurable, too) that might give what you want. I also use "SMarterContainers" for chest sorting. (Again, lots of configuration options to tweak how you like.) I don't know about bigger stacks, but I know my players have suggested several mods that do so; jsut not sure on the names. (I dodn't like the idea so shot it down without searching myself, heh.)
3) I use "OdinsCraftyBoxes" to craft from containers.

All of these can be found on Thunderstore; I recommend using the r2modman mod manager, but THnderstore Mod Manager is essentially the same.