The nursery person was right, the silvery stems are dead. You can cut them out. Crispy leaves this time of year is also not a big deal. Expect the leaves to be crispy from mid summer on. My concern is the part of the tree that's dying - those are major branches, not the little twiggies that normally die.
My bigger concern is the size of tree you bought. It has been proven there is no benefit in buying a larger tree. By the time the larger tree acclimates, a smaller tree has caught up and is healthier.
Transplanting a JM still in leaf is also risky. If the rootball breaks up at all, shock could kill the tree.
JMs are not usually pruned as their shape is beautiful. Only dead and crossing branches are pruned. The minute you prune, you ruin the shape of the tree. The branches that have alreay died back are going to affect the future of the tree.
My best advice would have been buy a 5 or 10 gallon tree with a nice shape and watch it grow.
