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.
I just purchased my first Japanese Maple, and I noticed some of the branches at the top of the tree are silver. The nursery told me to prune them, but I wanted to check with forum members first. The nursery said the maples get stressed in central Texas while they are in pots, and many of the leaves were looking a little crispy. The nursery said the tree would be much happier next Spring after it acclimates to the shady planting bed where the tree will live. Any thoughts? Should I cut off the silver portions? Any other pruning tips after I get it planted tomorrow? See attached photos. 
