Don't know if it happens so much with JMs but with some trees,when multiple branches/trunks grow surrounding one in the middle,the central one often dies off as it gets harder to keep it supplied with nutrients etc.as the other branches grow.The other trunks have overtaken the central one so maybe it was gonna happen one day anyway.I expect the stump is dead now so wouldn't worry too much about dark patches.
Not sure about the green stuff,could it be just harmless lichen?One of the resident experts will be along to throw light on the whole situation I'm sure :)
As for the seedlings,just dig'em up carefully when big enough to handle and plant in a free draining container and position in a sheltered spot 'til bigger.

Thank you houzi! That's a lot of good info. A local gardening group also identified the lichen and miss and said it was no big deal.

I'm very relieved! That makes a lot of sense about the center truck. I have a lot of learning to do but you guys are so wonderful to help out like this. Thank you!