AZL, it is a huge comfort to have you here as we try to decipher all of this - thank you!
Answers in red below. 
So my legal question(s) -
I understand the logical, legal reasons you have so patiently posted as to why the 'mystery witness' is not likely JA, nor a paid expert. However, Is it possible that JA, or her team stated to the judge that she needed to testify to something, perhaps not entered in the guilt phase, but would only do so in secret? Is it even possible that they argued that because her life is on the line, that any testimony she gives is can be considered potentially 'life threatening"?
I know anything is possible, but is it legally possible to argue that?
It's possible to argue it, but not with a straight face or with the support of any legal authority.
Is it possible that JA needed to testify in order to have another witness testify about something, that is highly controversial, that would allow for the secrecy?
Yes--not for something "controversial" but, e.g., for something that might harm a living child or reveal the identity of an undercover cop.
If so, would that be an issue if it was later found that further information was available, but not able to be presented because the secrecy precluded it? For example, if JA stated TA had been somewhere, but a friend realized after the fact that TA was with them, or out of the country, or something?
I think you mean would it be a problem if JA/secret witness X lied and no one knew because it was done in secret? IMO yes.
Could a witness state they felt threatened if an aspect of their personal life were to be brought up in public court? If say, they had a criminal record, or were frightened they could be charged with perjury?
You can state whatever you want. But it wouldn't be grounds for closing the court. Especially the perjury issue lol!
Last one - if Juan did not contest the sealing of motions & orders, and/or the non-public courtroom (which it sounds as if he might not have, in the interest of getting this done), would Judge Stevens had to allow it, as there was no argument against it? Hence the media argument in front of COA? Is JSS obliged to abide by COA ruling, or does she have the right to interpret as she sees fit?
JSS is obliged to act within the confines of the US Constitution even if no one specifically asks her to do so. Also, the media did object, strenuously. And yes, she is obligated to abide by the Ct App's rulings.
Sorry for all the questions, but so appreciate your knowledge!
