My wife will have been in the UK on ILR three years next June
You really mean that? 3 years on ILR? Why hasn't she applied already?
Can you post when she first (legally) came to the UK? On what sort of visa was that? Any more visas issued after that?
If she did indeed get her ILR 3 years ago, presumably she has not yet passed the Life in the UK Citizenship test. She will need to pass that before making the Naturalisation application.
Documentation needed when applying? Isn't that clear from the form AN and the Guide AN?
By the way, are you British?
