Apparently she has quite some problems around the shoulder but you seem not to see a pattern. Limited external rotation will cause more strain on the ACJ. Impinchment how slight it is will cause an extra strain on the ACJ (altered movement to avoid pain).
I would suggest to look 1st of all more global and see if there are other limitations, poor control which could potentially influence the Gleno-humeral, ACJ, SCJ, Scapula-thoracic area.
Example; poor mobility of the neck and specific the CTJ will influence Scapulo-thoracic movement (Ribs have to slide in their vertebra joints to allow excessive movement as happens with crawling) Poor Scapula stability will affect the correct position of the Glenoid joint and the ACJ. Poor Scapula-thoracic mobility would do the same. Examples: reduced length of internaL rotators as Pecs (major and minor), subscapularis and Lattisimsu Dorsi (the latter is the worst!) will cause protraction and depression of the shoulders which cause the Gleno-Humeral joints point anteriorly more than laterally, thus causing internal mis-alignment of these joints (head ofhumerus is translated anteriorly). Poor strength of the lower traps and Serratus anterior causing poor Scapula control by winging in different ways (look at winging from flexion and/or abduction to neutral of shoulder, I bet she cannot control).
Also to test patient on hyper mobility (which would mean she needs excessive retraining on control before even considering strength training.
Anyhow lots of work to do. I do not think the problems you point out are separate problems and I could even imaging she might have very tight rotation and sideflexion of the truncus.
In short: 1 look at movement patterns of the shoulder girdle and spine. analyse the reason(s). 2 check muscle length 3 check stability issues. 4 check for hyper mobility 5 check neural mobility. Do realise that swimming has atendency to provoke an increase of mobility and that therefor coordination around a joint becomes far more important (compare to stability after shoulder luxation).
Hope this helps.