Reading this, my gut is saying SIJ isn't the issue (i.e no true fixation).
With the supine-to-sit test, if there is an apparent LLD (leg length discrepancy) in supine but not in sitting, my thought would be that there is some sort of myofascial restriction that is causing the LLD to appear. The fact that the apparent LLD disappears when they come in to sitting would say to me that the SIJ itself is rotating as it should.
What other SIJ tests have you done....list them all with their findings and maybe we'll see a pattern that will help. (i.e. both mobility / kinetic testing and stress (pain provocation) testing).
HOWEVER...has she noted any difference when wearing the SIJ belt (either related to pain or function)?
When she heard a pop in her "hip" what do you mean by hip? i.e.....do you mean the actual hip joint or do you mean in the gluts?
What were the findings of all your resisted muscle testing?
Other than pain with F/Add/ER, is there any other positions that she has significant tightness either bilateral or compared to the left?
Since she still ran another 21 miles after the initial injury, it would have been very inflamed so would expect a little more time for things to calm down. However since this happened in February, she should be past the point of pain related to inflamation. Findings may be there at the SIJ but again, my gut is saying the it's the compensatory factors related to an initial muscle strain that's making it look that way (but of course, I'm not the one looking at her!! )