Hi Brendansarah15,
Firstly I'm sorry but I couldn't see the actual grub screws in the photos of the clutch and as such I thought they might be missing, but that's not the case here.
Now looking at your initial photos again it seems that there is a engine, clutch and shaft alignment problem.
Can you tell me that when you pull the starter rope does the clutch rotate totally in line (concentric) or is there some wobble associated during the rotation ?
Now as far as your sharpening is concerned it appears that your bed knife is no longer serviceable (going by your photo) as it's not straight on the engine side of the mower.
The basic fundamentals of a cylinder mower are that the blades on the reel must all be equally gapped all along your bed knife. In your case no amount of back lapping or sharpening will solve this. You need to have this bed knife removed and replaced by an engineer and only then can both the reel and bottom blade be sharpened and re installed correctly into the mower to obtain the correct mechanical alignment.
Cheers,
BB