You are correct. Your wife is eligible to apply 90 days prior to the three years anniversary of the grant of permanent residence.
The requirement is for three years of permanent residence after lawful admission, which period would commence, according to the dates you provided, in November, 2003, meaning she could apply three months prior to the three years anniversary date, or 33 months after lawful admission, August, 2006 - last month.
The three years' lawful permanent residence requirement can be tolled, or broken, by voluntary absence of six months or more.
Don't confuse the requirement for three years "continuous residence", with the six months "voluntary absence" restriction - The controlling statute clearly refers to voluntary absences of periods of six months or longer, not to a cumulative absence of six months or longer.
The issue is that longer absences - without intervening return to the U.S. could either (a) indicate lack of intent to reside here permanently, or (b) allow the required "attachment" (i.e. affection) for the U.S. to lessen.
In any event, the three years of continuous residence can only be broken, in the context, by a voluntary absence of six months or longer - The total number of days or months of absence duriong the three years is irrelevant, so long as the applicant's intention to permanently reside in the U.S. after citizenship is acquired never fails.
For example, an alien lawfully admitted in November, 2003, could return to his or her nation of origin every two weeks, and stay for a week at a time (so long as the reason for going back did not indicate that the applicant did not intend to reside here permanantly), for the entire three years. That would equate to absences totalling almost nine months during the three years, but it would not matter. The applicant was never had a particular absence long enough to toll the three years period. The total number of days absent cannot be aggregated.
You can learn more about this by reviewing CIS Interpretation 316.1, which is available on the CIS website at
www.CIS.gov.
But more importantly, there is a statutory provision expressly exempting the spouse of a U.S. citizen whose employment results in his or her being permanently assigned overseas. You can read Section 319(b) of the Immigration Act (codified as 8 U.S.C ss.1430(b), or, read an official summary in simpler language at CIS [Interpretation 319.2.
Put simply, probably neither the three years "continuous residence" requirement, nor the six months "voluntary absence" restriction ever applied to your wife, because she lived with you, a U.S. citizen, whose employment resulted in his being permanently assigned overseas.
Hope this helps. Good luck.