your wife needs to have been in the uk 3yrs to the day UKBA receive your application, not any sooner..
Here's the detail jhon

The residential qualifying period will be worked out from the day we receive your application. Most unsuccessful applications fail because the applicant was not present in the United Kingdom at the beginning of the residential qualifying period. You must make sure you meet this requirement before you make your application. For example, if we received your application on 25 November 2005, you would have to show that you were in the United Kingdom on 26 November 2002.
Of course, if you're confident your applications are fully compliant the apply by post.

The 'old fees' are:-
£851 for single appl
£1317 for Joint Appl

The 'new fees' will be:-
£874 for single appl
£1550 for Joint appl

Applications made prior to 5 April 2012 will be at the 'old fees'. Means actually received by UKBA before 6 April 2013
6 April is a Saturday. Personally I'd want my application to be received and stamped by the UKBA post team on Friday 5 April 2013
It is based solely on this date of receipt, not on any date that the decision is made.
I'm not sure where this 4 weeks processing come from. Processing may be longer or shorter than 4 weeks.

Just be sure that when UKBA receive and stamp your applications that they are fully compliant and meet the rule stated above.
UKBA are often 'unfairly' strict on dates

What is the date for the START of the qualifying periods for you ALL ( read the rules)