Yo Ben! Thanks for giving it another shot. I appreciate the feedback. Meshing the puzzle UI/UX in with the combat has, hands down, been the most challenging part of developing 4TONS. I'll definitely take this all into consideration!
In the default control scheme, picking up the staff and entering a portal are both bound to the interact key, F. There's a slim chance your old custom keybind profile from a previous build might be giving you a weird experience . In the Main Menu, go Settings -> Controls -> Reset to Default and try going through the tutorial for the new controls.
The staff and inventory was previously one page, but it's been consolidated for screen real estate in co-op, and I did the same in single player for consistency. I understand the friction there, so I'm brewing up a few other creative solutions to the problem.
Clicking on an item on the ground can't pick up items, because left click is your primary attack, as it is in every Shmup. This would likely result in accidentally picking up a puzzle piece mid combat and getting ganked.
Give it another shot with the default keybinds (or a controller!) and let me know your thoughts.
Thanks!