1964 Kennedy Half - Black Schmutz! Help!

Are these business strikes? How did you obtain them and what were they in before you put them in the cardboard flips? By "hard plastic covers" do you mean polypro "safe-flips"?

It looks like the tarnish is from hitch-hiking skin oil or bacteria. IMHO

Try a dab/press (not scrub motion) with q-tip w/vinegar, @5 seconds max, then rinse w/ clean(filtered is better) water and tap dry w/ very soft (lintless preferably) cloth. If it is something more that acetone won't remove (organic) the a weak acidic such as vinegar might help, although, any acid has the potential to do worse damage.

On stuff like that I try 1) soap & hot tap water, fingertip motion. 2) acetone. 3) vinegar tap 4) vinegar soak (50% vinegar, 50% hydrogen peroxide)

I put them in my safe deposit box along with the rest of my silver and coin collection. They're all stored vertically and separated. But about three years ago, I put my copper coins (ie wheat pennies) in paper rolls. These Kennedy's were in perfect condition. I never had a problem. I'm sick to think of what happened to them. It's got to be environmental. Would their close proximity to copper cause this? They were flawless. Not any more.

Copper should not cause a reaction unless in direct contact with each other. Safe deposit boxes in bank vaults are environmentally controlled low humidity, constant lower range temps, just for the protection reason. How long ago were these placed in 2x2's? Did you use gloves when handling, handle only by edge...factors prior to storage may have just taken time to show up, once started tho goes fast. I would get these bad boys out of their current home and try an acetone bath. If that is a mold perchance, that will clean it. I image it is a tarnish, caused by handling, not necessarily you, but all before you got the coin.