You have keen eyes to spot those tiny dots!
Junipers can get scale insects that look a bit like black/brown/whitish dots but they live on green leaves and can be hard to spot until there are many. I suspect that
@Wires_Guy_wires is correct about fungi on the dead parts but please check live areas just in case.
The second picture shows callus growing over a wound. I guess a small branch broke off there at some stage. Healing up cuts is a good sign the tree is healthy and growing.
Adding a location to your profile will give us some help when making recommendations as timing, pests and treatments can vary depending on what country or climate zone you live in.