HOW do you rotate (switch?) the input and output? During startup of the game or realtime in game? If the latter how? Via a button? A key press?

On startup, It creates a new hidden recipe with the fluids permuted.
Then, in realtime, when the player press the key bind, it gets the selected building, see its recipe and its permutation.
Then it gets the previous/next permutation recipe and it sets on the building.

Please add that description to the mod page and maybe show an image of it in action. (How many permutations does it generate? One flip for inputs and outputs each, same as GDIW, or more/less)

is it better now?

Yes, thank you.