Most likely this is not a pest or disease. When plants decline in the months following planting it usually is an abiotic problem (not related to insect or disease). Quite often the roots of these junipers become very compacted in their containers at the nursery. When the roots are very compacted it makes watering the shrub more difficult. A very tight rootball actually repels water. However, it is true though we have had a lot of rain which can also be a problem.
If you want to give this juniper a chance you need to prune out the brown stems and needles. If the root system was compacted and you did not break it up before you planted it consider digging it back up.  Then use a sharp knife or blade to cut four one-inch-deep cuts the length of the root ball. New roots will rapidly grow from the cut areas of the roots. When you have to water do not just water the top of the shrub with a hose but direct the water near the ground where the roots are.
It is questionable whether that area will fill in again. 

Deb

Thanks. I will trim out the brown and re-plant per your instructions. What is a typical pattern of growth for Junipers? Do they tend to grow new stems and needles or just get bigger with what they have. if the latter, I may want to get another plant that doesn't have a hole (where I already pruned out some brown stems). What do you think?

If you can the best thing would be is to replace it.  Digging it up and replanting it will set it back and then you have to wait until next spring for the new growth. Score the roots of the new one and water it properly. 


Deb