I'll tender this. Try Specialized for shoes. I believe at the Comp level you can get a wide width. I schlep 9 1/2 EEE footsies. I have a pair of comp MTB's in 44 wide. They work great. Lots of room. As a matter of fact just slightly too big. I have the Comp road shoe in a 43 1/2. They are really snug. At times I do get some pain in my left foot.
Shimano also has some wide width shoes. Other than that there are SIDI's ($$$$$) and a few others that are hard to find. I'd give the Spesh's a shot. I have some fairly serious arthritis on the back of my patella's. I have no problem clipping out of either Shimano SPD's or the road SPD-SL's. I think another choice would be to look into Speedplay pedals. I forget the model but you can get adjustable clip out angles. You can literally adjust the float. May well be worth a look see.
I think a clipless pedal setup would be the best. I don't think you're knee will be bothered by a good set of shoes and clipless pedals.