As said, you can apply directly and the form for naturalisation applications (form AN) has a specific section (2.4) for these cases. The
Booklet AN (see page 33 onwards) is quite clear on that.
You can apply on the 6th anniversary after you have been living in the UK under EEA regulations. This means after your wife started exercising treaty rights. Not you. So some time after Feb 2012 depending on your wife activities.
As your case is not a standard one (a switch from WP to EEA during the 6 years), I suggest you add a cover letter explaining why you have obtained the PR automatically. There is no need to involve a lawyer. Just make sure you provide the needed evidence (5 P60's is the simplest if your wife worked throughout the period) and a cover letter.