Hi Blaze.
I think Nichole has provided a reply that is incredibly thorough and yet to the point. I am envious.
In the Ashtanga series there is typically an abundance of Chaturanga Dandasana in that version of Surya Namaskar. While I do not teach or practice Ashtanga, I have taken enough classes in the first series to know that much.
We choose our practice for a reason, sometimes unbeknowst to us on the conscious level. Since you have elected to find yourself through that practice then the most sound answer should blossom from the teacher to whom you are entrusting that growth.
The Ashtanga practice was intended as a practice for youthful, slim, fit, agile students with furtive minds. Obviously there are things we can do as slim 19 year olds that are much more “challenging” to do as robust 35 year olds. The muscles of the rotator cuff; supraspinatus, infraspinatus, teres minor, and subscapularis not only work together but they are somewhat fragile in nature. They can be built a bit but they can also be easily damaged.
If your situation is only one of muscular endurance in Adho Mukha Svanasana then of course this will build over time in your practice through phalankasana, bhujangasana, urdhva mukha svanasana, sirsasana, vasisthasana, urdhva dhanurasana, adho mukha vrksasana, and pincha mayurasana. Keep in mind you’ve been practicing less than two months and this is an entire art to learn at every level of your body (speaking physically only for this post, thank you).
If, however, you are experiencing pain in the shoulder joint, or are placing “excessive” load on those four muscles I mentioned, then it might be best (in terms of safety over time) to modify Chaturanga in the plethora of surya namaskars that you are choosing to execute.
Generally speaking, due to the angle of the body in AMS the work is not entirely in the deltoids (which you reference when you say “my shoulders”). But it is not at all unusual for there to be challenge in this sort of supporting at this stage of your practice. If this is still occuring 6 months from now then a different reply would be warranted.