Although you have raised some good points regarding the possible shooting down of flight 93 (I agree with you that it was probably shot down), your assertion that the use of the phrase “primary target” in the ATC transcript supports our suspicion is probably mistaken.
It seems that the phrase “primary target” is not necessarily military, if you read the NY Times report.
The civilian Air Traffic Controllers use that phrase to refer to any aircraft which does not have its IFF transponder switched on.
I have already had an email from a colleague ridiculing your theory simply because of your “primary target” point.