Re: Removing non-footied apples
My vote would be "yes, if you have the time and / or the desire.
If you live in an urban setting, you are not likely to make too much of a difference to the codling moth population of your tree (which you say is your big problem).....because the codling moth flies a fair distance and is still likely to come in from a neighbor's property.
You would make a bigger difference to any apple maggot problems you might have as this is a lazier insect that comes mostly from the soil right beneath your tree and by sanitizing your tree you make a very big difference to the immediate location of your tree with apple maggot fly. (but you don't indicate this is a problem).
However, here is where you make the biggest difference....by eliminating the other apples you ensure that the apples that you do have left inside the foot sox will become bigger....and maybe better.
so, yes, I would say get rid of the others.