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There is so much literature about working with organizational hierarchies and methods to monitor them and measure performance, but in reality teams behave more like (heavily) cyclical graphs, especially in organizations that don't have a "silo mentality" and promote common ownership.
Are there any best practices for cyclical graphs?
Have you looked at Systems Thinking at all? In its application to work it addresses issues of common ownership of purpose, how you measure the effectiveness of an organisation in achieving that purpose and the methods they use to improve that effectiveness.
I was introduced to Systems Thinking through the work of John Seddon who is focused on Systems Thinking for Service Organisations.
Karl Scotland writes about Systems Thinking and Software Development here with specific reference to John Seddon: Systems Thinking, The Vanguard Method and Software Development.
To your point of "trying to measure the performance of teams, by monitoring the total output in specific fields."
Have you come across Don Reinertsen's criteria of a good metric?
He sets these out in his book 'Managing the Design Factory' as being simple, relevant and focusing on leading indicators, in your case future performance.
In the software projects I have worked on the two most useful metrics I have found are taken from Kanban; Throughput and Cycle Time. Throughput is how many pieces of value work, features, stories etc, a team produces in a given time period.
Cycle time is how long it typically takes for these pieces of value to be realised; measured from the point they are pulled in by the team to start working on them to the point where they are delivered to the customer.
These are very much focused on output; 'What has actually been produced?' and performance 'How long does it take to produce it?' so may be a good match for what you are looking for.
