Using the provisions of para 287(a)(i)(d) of the Immigration Rules the period as a dependant of a Tier 1 holder can be used towards the 2-year qualifying period for ILR. Accordingly she can apply for her ILR from 28 days before the 2nd anniversary of her arrival in the UK.
That assumes of course she has passed the Life in the UK Citizenship test, or got a completion certificate from a combined ESOL/Citizenship course.
Using the numbering in your opening post above :-
- You are right about the 3-year qualifying period, so she cannot possibly apply for Naturalisation until after the 3rd anniversary of her arrival in the UK.
- Yes !
- You have a choice. Firstly you could apply as soon as you have had your ILR for 12 months, and then if that is granted, your wife will be married to a British Citizen, you! Accordingly, and assuming she has ILR, she can apply for her Naturalisation as soon as she meets the 3-year qualifying period mentioned in 1. above.
Secondly, and again assuming she has her ILR, a joint application could be made as soon as your wife has completed her 3-year qualifying period. But if you do that, you must send a covering letter asking them to process your application first, and only assuming that is granted, then ask them to process your wife's application. The point is that the qualifying period is 5 years, unless the person is married to (or in Civil Partnership with) a British Citizen.
Given the way application fees keep going up, my personal choice if I were in your circumstances would be to make a sole application in January 2013, and then for your wife to make a sole application when she is qualified to apply.