In the guide an naturalization for british citizen it says there that if one is a spouse of a british citizen, one has to be in the uk for 3 years before they apply or else they will not meet the requirements (though in the span of 3 years one is allowed to leave the uk for certain numbers of days before applying for ilr and also for citizenship).
As in your case, due to the 28 days that was being allowed to apply your ilr was granted earlier. In my opinion i think to be in a safe position, so that the one who will process your application for citizenship will have no excuse to refuse you, better to really adhere to the ruling and that is 3 years period beginning when you arrived here in the uk regardless of the granting of your ilr.
I done mine by post you see, so my ilr was granted a few days after my 2 years here in the uk then, so my citizenship was granted a year after my ilr. So to be safe apply on 19/12/2012. As for the birth certificate if you do it by post with no checking services better to send passport as well as birth certificate, the uk border will have all your relevant documents and it eases your mind too that you provided them with everything.