This issue got quite a bit worse, and after doing some research I'm pretty sure that it's Phomopsis Twig Blight.

It spread to the rest of the foliage and has also spread to the rest of my shimpaku juniper.
I read some sites that had info on it, and based on their recommendations I have cut out all of the blighted twigs and branches(which really didn't help the look of any of them) and sprayed them all liberaly with a copper based fungicide.
I'm really bummed out about this. If anyone here has had any experience with this blight I would really like to hear what you know about it, and what experieces you had dealing with it.