How should I deal with the FAA and IRS?

What does the Federal Aviation Administration have to do with the IRS??

How do you deal with two completely different unrelated federal agencies? If your problems with these two agencies overlap with each bureaucracy consult a serious big-time attorney.

For such a general question, all I can advise is keeping complete records of all corrospondence and phone calls. Never say or write anything you don't want to hear repeated, and never threaten them, not even with legal action.