Thank you for contacting Ask Extension. The orange growth is called cedar apple rust. This is a fungi that happens when one plant from the Cupressaceae family (red cedar, juniper) and the other from the Rosaceae family (crabapple, hawthorn, serviceberry, etc.) are within range of each other. To prevent this, make sure not to plant junipers within a few hundred yards of any of the Rosaceae family. After they release the spores, the galls will fall off. You can prune out the diseased area if you choose, but the cedar apple rust will not harm the juniper. And if you prune it out, then the chance for reinfecting the juniper next year will be lessened. No fungicide will control it because it is an airborne fungus that can spread up to 1 mile away. 

The brown on the lower branches appear to be  Winter burn which occurs when winter sun and wind cause excessive needle water loss while the roots are in frozen soil and unable to replace lost water. This results in desiccation and browning of the needles. Wait until mid-spring before pruning out injured foliage. Brown foliage is most likely dead and will not green up, but the buds, which are more cold hardy than foliage, will often grow and fill in areas where brown foliage was removed. If the buds have not survived, prune dead branches back to living tissue. Winter burn can be reduced if evergreens are kept properly watered throughout the growing season and into the fall and mulched.

Here are some references for you:

 http://www.extension.umn.edu/garden/yard-garden/trees-shrubs/protecting-from-winter-damage/

https://extension.umn.edu/plant-diseases/cedar-apple-rust

https://www.canr.msu.edu/news/cedar_apple_rust_disease_on_junipers

https://hort.extension.wisc.edu/articles/winter-burn/#:~:text=For%20evergreens%20such%20as%20arborvitaes%2C%20boxwoods%2C%20junipers%20and,affected%20branches%20and%20look%20for%20green%20tissue%20underneath.