My experience with collected junipers is terrible to say the least. I collected 5 smaller Western junipers (1' trunk) last fall and they all died. They were collected with a good bunch of roots right below the surface but then the long tap root was cut off. Planted in correct soil and were left out for winter and watered occasionally as needed. All dies this spring. No misting and maybe to much water along the way. I have numerous nursery purchased Western Junipers that do fine with me. From what I have read, I think junipers like moisture around their foliage area after collection. Because of my weather situation (zone 5-6) I was unable to do that. Better off collecting in the spring I think.
In regard to bagging collected trees, I have always seen the entire pot and tree bagged to create humidity for the tree. The color and type (mm thickness) of the bag is important too. Heavy black bags can create a lot of heat depending on the sun. As one gets warmer temps and more sun in the spring, I have found, with spring collected hawthorn, that it pays to switch to a lighter (0.95 mm) black bag. This cuts down on the heat and lets in sun light where the heavier bags (3mm +-) let in none. I have taken collected hawthorns that I have taken out of the heavier bag because of heat that are really struggling to produce foliage and put them (the tree and pot) in the lightweight bags mostly sealed, and the new foliage starts to roar. If the weather gets to hot, creating to much heat again, I switch to a HD white bag like the ones you would put in a compactor and put the trees in morning sun. We now have way less heat but still the needed environment for growth. I still mist every day, watch for fungus, and open the bag more and more with time and foliage growth. Has worked worked for me.
Just my thoughts and experience. This might work for your junipers that are struggling. Wish you the best OP.