I was refering to 'physically present in the UK for 3 years if you are married to or in civil partnership with a British citizen' criteria .
Again there is no criteria worded exactly like that.
I suspect you are referring to the need to pass the "applicant was physically in the UK
exactly 3 years before UKBA receive the Naturalisation application" test. As you tell us "She entered UK for first time in Nov 08.", she will start to pass that test some time during November 2011. Just make sure the application is submitted after the 3rd anniversary of her arrival in the UK.
As regards whether you need to be in the UK when your wife applies, you need to appreciate that your wife needs to prove that you are a British Citizen. Ordinarily that is done by the spouse supplying their British Passport, but if you will be out of the UK that would not be possible. However if you were born in the UK then instead it is possible to supply your full birth certificate to prove you are a British Citizen.
But you tell us you have Naturalised as British.
From the UKBA website :-
Documents required for applications made on the basis of marriage or civil partnership to a British citizen
You should provide:
your partner's passport or birth certificate; and
your marriage or civil partnership certificate.
But as your birth certificate will not prove you are British, it follows that your passport will be needed, and accordingly you will need to be in the UK when your wife applies for Naturalisation.
Suggest you fly back to the UK for a few days, attend a pre-booked NCS appointment together, then your passports will be copied and handed straight back to you, after which you can return to the country of your employment.
