I think a band-aid fix that might be helpful is adding plain text descriptions of the controls with the tutorials. The little pictures are helpful for more common mechanics but because of how specific these are just a static visual isn't always super clear on what it means (specifically for me moving blocks was an issue--I thought you just couldn't for a while, the right click icon seemed to me like it was meant to be used just to select a box).
As for reworking the controls as a whole, maybe something like logisim where boxes are locked onto a preset grid? Using different length "wires" between nodes could be a more intuitive way of staggering actions than using Do Nothing as a buffer. It would also negate the need for moving them, as any node could be just set back to empty using 0. Though I have no idea how appealing or feasible implementing this would be, as restricting the amount of space would force you to change the screen layout or limiting player freedom to a smaller space. The controls you have in place, while a bit hard to work with, do not add undue difficulty to the puzzles themselves, which were still a fun challenge per usual.
Another small note is that I kept getting frustrated with the automation of the order of connections (how you always have to draw New Thing and Yes first, and deleting a New Thing or Yes connection automatically turns the Old Thing or No into its opposite). If it doesn't mess with your existing code, I think an option to pick which one you draw when you ctrl + click the initial node would be appreciated.
Sorry for being so long-winded over what are ultimately minor gripes. I love this series, can't wait to see what you do next!