Problem
The upstream server is timing out and I don't what is happening.
Where to Look first before increasing read or write timeout if your server is connecting to a database
Server is connecting to a database and that connection is working just fine and within sane response time, and its not the one causing this delay in server response time.
make sure that connection state is not causing a cascading failure on your upstream
Then you can move to look at the read and write timeout configurations of the server and proxy.