Last summer (2017) was cold, wet and miserable. 4th of July I spent driving fence posts in the rain with my Carhartts on because it was so cold. It rained and was cool pretty much all summer.
In the spring, I had planted 6 apple trees (on Antonovka), haskap, sour cherries and some various other fruit bushes. They struggled due to all the water, and put on very little growth. One of the apples got fireblight really bad as did the Evans cherry. At the end of the summer, it got hot, and all the plants started putting on growth - when I think they should have been going dormant.
Fast forward to this spring. The one tree that had fireblight the worst I had to cut down to about 6" tall. I didn’t think it would live, but it shot out new growth like a monster from the 6" stub I left. It’s all above the graft (which I did bury) so it’s the Blue Pearmain. I lost the tops to all the apples, some put out a couple leaves in the branches, then those leaves died and they started growing from the bases (all above the graft) like mad.
I lost a Romeo and the CP (which was puny to begin with) and oddly, a 8’ tall sugar maple that had been in for about 4 years. I left everything in to see if it would sucker or show some sign of life, and the maple did send up a tiny shoot at the base of the trunk this week. The cherries are dead, dead, dead.
So my question is, how do I salvage and train these apples? I don’t want to create a disease magnet, all the new growth right now is about 6" off the ground and I think the first branches would end up on the ground at maturity. I’ve seen the “tiny” apples, but this is a bit extreme 
. Should I choose a leader and prune this winter… or should I pick one now and remove the rest? The growth is about 6" long at this point and on most trees I’d have 5 or 6 growths to choose from for a leader. I live in 4b and we had a really late spring, so things are just kicking into high gear here now.
Thanks for any suggestions.