I contacted Colin Lewis about the problem and here’s his suggestion;
Many junipers become purple when cold dormant, but that’s not going to happen where you live. My hope would be some vascular damage that affects the lower branches on that one side is responsible, and a redesign would solve the problem. But I see there are smaller outbreaks within otherwise healthy branches, which does indicate fungal issues.
First, I would cut out all dead and dying branches - right out, leaving tiny jins at best, and sterilizing the blades after each cut (Zerotol or alcohol and fire!). The two go-to fungicides that I use are Daconil and Mancozeb. I also use a product called Zerotol which is anti-bacterial as well as a fungicide. This should also be watered into the soil to combat pseudomonas. It’s only available in commercial quantities - like 2.5 gallons, so it’s not cheap but well worth it.
I thought about it for a day then took my trusty cutters and removed the first small branch. I noticed that that small branch was not strong and was sort of spongy which indicated to me it was already dead or at least dying. I kept going and removed a larger branch, sterilizing the blades with alcohol and fire. I noticed the fungus - a dusty substance - was on my gloves. After finishing all the removal, I piled the limbs and greenery and burned them. Here’s a picture of the work;
I ordered the Zerotol today as I’ve already tried Daconil and Mancozeb with no effect on my problem. You are right-a little pricy. I am making corn water tea - to generate the Trachyderma, an organic fungicide - suggested by a local horticulturalist for use until your expensive stuff shows up.