Cable connection issues on the RPi camera can be very hard to diagnose. Glad you got it working.
I have not got a microscope in front of me, I cannot remember the filename. It is one of the microscope config files and I remember finding it quite easily. If this is a new build, it may end up being simplest just to start again with the operating system.
The current software beta release has a new camera calibration which solves the green issue. If you are happy running the beta then that is the best solution.
Edti: I have just found that I wrote this in another thread " sudo ofm reset sudo ofm restart will clear most of the calibration from the server and give the calibration a fresh start." that would not need you to manually delete the calibration.