That is a very fair complaint, the controls aren't the smoothest always (and I always need to double check what the combo actually was when replying to people asking for help). It seems that the controls are a big barrier for people when playing the game, and I kinda painted myself into a corner with how I designed things, like the shift + left click for taking stuff out the output slot was because left click was already in use for taking stuff out of the input stack, and that in turn is because I really didn't want inventory ui to be a thing in this game.
If it helps, the recipe book has a [ ? ] button that opens the controls cheat sheet. In hindsight it isn't the most obvious thing to click for controls help (given that it's in the recipe book), and definitely it should have been in the options menu as well. I can't fix it at the moment, but I could actually add the controls cheat sheet to the description for the game on itch.