Well I finally received a reply from the TSA dated 12/3/07.
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Good morning RSSrsvp,

I apologize for the delay in my response. Our office has received the paperwork on the initial incident from November 2nd. After discussing the situation with the Security Manager in T2, it has been decided that all parties involved will attend Customer Service Training.

The majority of the terminals in JFK airport do have video tape of the checkpoint. These tapes are the property of the respective airline operators. They determine the length of time that a video tape is kept. It ranges from 30 days to 3 months.

In response to your original question of photocopying documents, there is no policy that neither requires nor prohibits the photocopying of documents in matters relating to customer complaints or compliments.

Respectfully,
XXXXX XXXXXXX
Transportation Security Administration
Acting Customer Support Manager / JFK
230-59 Rockaway Blvd
Jamaica, NY 11413

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Sounds like a tap dance to me. Especially the part about photocopying my ID. I emailed them back and asked the following:

Dear XXXXX,
Thanks for your reply.

Regarding my main complaint, if there is an empty terminal as was the case with T2 on the morning of travel in this case and a passenger is waiting in a line for absolutely no visible reason, they are certainly within their rights to question the officer as to the cause of the delay. Delta's T2 which is reserved for their First Class, Business Elite and Medallion members is always empty that time of the morning and there is never a long wait at the TSA security checkpoints. In this case I asked TSA officer XXXXXXXX who was stationed at the initial ID checkpoint as to what was causing the delay. She immediately had a negative attitude because I had the "nerve" to ask her a question. This attitude was visible in her facial expression and her reaction was to send me to a secondary search solely for that reason. This was totally unacceptable and caused my response. Hence the writing of an official complaint form which was the first time I have ever done so in all of my years of traveling. I definitely did not feel any safer by her singling me out for that secondary search. On the contrary, her focus on me could have prevented her from spotting a real threat to the airport's security which is the main reason why she is there in the first point. Every TSA officer should be trained to properly address any passenger's question without fear of repercussion. "Rotten apples" ruin the image that the TSA is attempting to portray.

Regarding the issue concerning the photocopying of my documents including my license I have two simple yes or no questions for you because you have stated in your reply that the TSA has no official policy regarding this matter.

1) Does this mean that I was within my rights to refuse to hand over my license and boarding pass to supervisor XXXXX in order to receive an official complaint form from him? Yes or no?

2) Also if he does have the legal right to view these papers which it appears from your reply he doesn't, do I then have the right to refuse to let him photocopy them? Yes or no?
Sincerely yours, RSSrsvp