Yes, the technique of requiring the examinee to repeat the last word of the question is a counter-countermeasure. It's an attempt to prevent the examinee from engaging in mental dissociation, or thinking about something other than the question being asked.

I can't venture a guess as to your chances of getting a clearance with the present government agency or any other. But if the agency involved was either the CIA or NSA, which use the relevant/irrelevant technique, you should know that it is not uncommon for applicants -- even those eventually hired -- to initially be told that they are having problems clearing the test, to be pressed for admissions, and to  be invited back for one or two "re-tests."

Yes and yes. Details of your polygraph experience will have been entered into an inter-agency federal database called Scattered Castles.

To address your questions, respectively:

1. It's unlikely that the polygraph operator had any confidence that you were using countermeasures. Were that the case, you would likely have been accused of "manipulating your physiology" and badgered for an admission.

2. Yes.

3. Yes.