I have a Canon S9000

I have a Canon S9000 Printer, There are 2 problems.
First. When I print a Picture the Colours are not correct, and when I print in Greyscale Black comes out Black but the Grey comes out dull Red to Brown. If I do a Nozzle Check the Colours come out fine.
Second. When I bring up the Printer Status it does not show the levels in the Cartridges properly. I have read that there is a light that shines through a prism in each Cartridge to ascertain how much ink is left. I have taken the Main Cover off the Printer and I think this " Light Sensor " is on the left hand side. When the Printer is on should you see a beam of light or is it Infra Red or some else. I cannot see any light being emitted. Perhaps this Module has failed. I will be pleased if you can throw any light on these problems.
Many Thanks, Basil Dyer.