JM, welcome. As Jack and John pointed out, the arrangement that you propose for your M3s should work very well. Keep at least 3" of "breathing room" behind the rear port and have the front edge of the M3 slightly protruding from the shelf. Removing some books probably isn't necessary, but you can experiment, of course. Don't worry about having the speakers very close to one room surface as long as the distance of the woofer cones to the other two room surfaces(floor and sidewall)are different from that and from each other.
