Right crank arm feels uncomfortable After a loose bottom bracket and some prevailing knee pain I have made a few adjustments to the bike. I have managed to greatly reduce the pain in my left knee but the right still has some pain. I have noticed that since the bottom bracket came loose that my right foot if positioned the same as my left  will knock against the crank arm. I have to perch my foot on the edge of the pedal. I'm not sure whether this is something that could be attributed to a bending of the crank arm or something else?
Well, the thing to do first is to determine if the crank arm is bent (or loose/poorly fitted to the shaft).  

Prop the bike up and "pedal" it backwards with your hand (from the right side).  Observe whether the shaft of the pedal maintains the same horizontal alignment all the way around.  If the crank arm is bent then generally the pedal shaft will be "pointing upward" at the top of the crank cycle and "pointing down" at the bottom of the crank cycle, and you can usually both see this and sense it with your hand.

(Note that a bent pedal shaft can produce the same symptom, though.  But if the pedal shaft is bent it will be obvious if you unscrew the pedal -- the shaft will "wag" around as you unscrew it.  And either way you'll need to replace some components.)

It should be noted that, on bikes with 3 front sprockets, the right pedal sticks out from the frame slightly more than the left pedal, making your ankle slightly more apt to bump the right crank arm than the left.  But the difference is slight -- maybe 4mm.