You gotta understand that an output of one thing may very well be the input into another. What has to be done is the management of the linkage between them. You are not suffering under something unique.
You entire organization is nothing more than a single large process transforming inputs into outputs and containing multiple smaller processes doing exactly the same thing. Each "process" may have one or more inputs that must be converted into one or more outputs which may or may not need to be fed into another "process".
To easily understand what I am talking about just get a box of Jello (preferably cherry), look at the picture on the front...that is the desired output. Turn the box over and read the instructions. You will see the necessary inputs, the "product realization process", the monitoring and measuring requirements and the desired end result and hopefully customer satisfaction is the result.
What you guys do is not different than making that Jello, it's just a bit bigger with a few more extras.