Scout,

Regarding your questions:

1) The "review board" is the FBI HQ polygraph unit. Their scoring of your polygraph charts is very likely to be the same as the original polygrapher's.

2) I cannot offer advice regarding whether you should take any "re-test" (if offered). However, you should be aware that the results of "re-tests" are almost always the same as the first one. Think about it, the FBI polygraph unit cannot afford to be seen reversing many original decisions. To do so would tend to undermine their credibility. On the other hand, the fact that you already hold a security clearance might place you in a better position compared to most applicants.

Whether or not you decide to take a "re-test," you should definitely appeal your polygrapher's opinion in writing (assuming FBI HQ endorses the original polygrapher's opinion). Your FBI HQ file is a permanent record that will be requested the next time your security clearance comes up for a periodic review. You don't want to let your polygrapher's accusation that you lied go unchallenged. Your letter contesting the results (send it by certified, return-receipt mail) will be added to your HQ file.

3) If you do get the chance for a "re-test" and decide to go ahead with iit, then I think it would be prudent to adopt the "complete honesty" approach and respectfully disclose that you have researched the polygraph and have reservations about it. 

Your polygrapher will indeed have the records of your first polygraph examination. Moreover, FBI polygraphers must expect that anyone who has failed their initial polygraph and been scheduled for a second one will have done some research, and they might understandably have a hard time believing anyone who claims they haven't.

Whether or not to use countermeasures on any re-test is a choice that you'll ultimately have to make for yourself. But if I were somehow compelled to take another polygraph "test," given the invalidity of polygraphy and the availability of proven countermeasures, I would not leave the results to chance.

Before any re-test, you might wish to seek a consultation with Washington attorney Mark S. Zaid, who is representing a number of clients who are suing various federal agencies (including the FBI) over their pre-employment polygraph screening policies. Filings from these cases are available here:

http://antipolygraph.org/litigation.shtml#zaid

Mr. Zaid's phone numbers are:

(202) 223-9050 (work)
(202) 498-0011 (cell)

Having had an experience not entirely unsimilar to yours, I can understand your reservations about working for an agency that would judge your honor and integrity on the basis of voodoo science. (See my public statement, "Too Hot of a Potato: A Citizen Soldier's Encounter with the Polygraph".)

I wish you all the best. Please feel free to contact me privately if you like.