I love it when people ask for "colours that mean..."
The first thing I always have to state is that you should never use colour alone to indicate status, purpose, or function. Doing so will mean your systems is close to unusable for any colourblind users.
You should be using iconography if you need to indicate flow direction and manipulability.
I'm unsure why you can't drag an output to connect with an input. I moonlight as a music producer and see this on interfaces all the time: the goal is simply to connect an input with and output - it shouldn't matter which order the user does this.
Here's a screenshot that has many similarities with your scenario (input, processing, and output) but doesn't care which order the connections are made:
You can see that the lines are colour coded to make them easier to follow but the connecting points are simply sockets with no indication of which you should click first. This is because, as a user, I don't want to have to think about how I connect things together - I just want to get on and do it. It shouldn't matter if I connect output to input or input to output.