I don't know what the issue was on the pH port. Do you have a way to hook the module to a computer with a SID to see if it has the current firmware? If you can update the firmware if it is not current. You can use PortCalibrate() command with the pH port once you get the raw data readings at 7 and 10. To use port calibrate you will need to know your module number and the port number of the port you are calibrating. To find that pick a unused output and select the controller function then show. Select the input. There are numbers at the left of the different imputs like "3:4" The first number is the module number and the second is the port. I think most of the modules with pH ports it will be port 4 with the exception of the Archon and the second port on the SLX. A port calibrate command is PortCalibrate(Modlue Number port Number,Low Calibrate Point, Low Calibrate Raw Data,High Calibrate Point,High Calibrate Raw Data).
Example: PortCalibrate(3:4,7.00,1050,10.00,-799)
This goes into the command line on the system page. It can also be used to do a two point temprature calibration on the temp ports. It has been awhile since I used this so I am going from memory. Lindsey or Eric if this is wrong then please correct me.
Your salinity raw data is not that far from mine. I did find out if you do a clean on it it is best to wait for several hours before calibrating it. I calibrated mine right after cleaning and it climbed to a reading of 47 before settling. It took about 24hrs.