Thanky for the compliments, really appreciated. And for taking the time to give such thoughtful feedback.
To your first point, it might be a good idea to let the (!) mark jump to the right side grid panel (or a marker with a mouse cursor, to advice the next action), as soon as player interacts with the branch. In that case, the marker would continue guiding the player to the next step as it has done before.
The limited inventory might prevent players in unlucky cases to pick a token that is needed in a certain moment. I was thinking of "unlocking" the interaction with certain items only in the moment, when the corresponding quest had been started. What you think?