There are two 1.3 mW generators 20 miles from my house. They have been using PRB coal since the mid 80s. They are located in southern Indiana. Coal rides a train to the Mississippi River where is is barged down the Mississippi and then up the Ohio River. They stock pile about 60 days worth.
I think all of the problems that you mentioned have been solved years ago.
Not so long ago I was talking to someone who was still working on the problem. As I said utilities use preventive measures such as moving piles around to minimize the buidup of heat in the interior of the pile. Depending upon the specific coal it could be safely stored for ten to fourteen days.