A: You can demonstrate the point by saying:
1. present and future project need you to collaborate extensively with someone outside your research institute. Therefore, LC, which require one fixed employer, can't be applied to you.
2. You need to get GC quickk due to the necessarity of traveling abroad.
3. It is impossible to quantify your research work due to the uniqueness of your research ability.
4. You can't work for some very important project due to the restriction of employment which require GC.
Q: Submit further documentation that shows the beneficiary's skills as being unique and innovative and of genuine service to the national interest of the United State. Does the beneficiary possess any special skills, .....
A: You need to establish this point with strong independent recommendation letters, saying you are well beyond anyone else in the field and without you, there is going to be a big vacuum in this field, etc.
Q: In support of meeting the third prong you have submitted numerous reference letters. In the reference letter ... " ..." however, this letter has failed to show how your research as already been used in academic and commercial...
A: Get some professor (independent) saying that your reseach finding could be applied to their present research work. Be spcific.
Get letters from industry saying that your finding has high indurstrial potential, or is being applied to industry.
Q: All of the above letters are from the petitioner's immediate circle of colleagues, mentors, and collaborates. ....
It would be expected that an individual that has influenced the field would have extensive citation record. .... please submit evidence of the extensive citation....
A: Explain due to the time of your publication, it is hard to get extensive citation. However, due to the importance of your work, you get e-mail request directly from someone who never know you (fake some) and provide a list of people who are interested in your research work.
Q: Please submit evidence from independent researchers stating to the beneificiary contributions and the impact on the field.....
A: again, more independent recommendation letters. 5 should be enough.
That is all I can think about. You don't have too many things to do. Get 4-5 independent letters from academic, industry and international community. Also get a new strong letter from your boss to answer the questions in ITD.
I feel that your ITD is not too harsh. It is more like RFE. You have good chance of winning your case. However, I strongly suggest you getting a good lawyer ASAP. You really need a good coverletter.
Good luck.