Problems with the Cogito

I applaud Descartes in actually establishing something (that is not nothing) in his second Meditation and think he is getting somewhere, however, I also feel that there remains a large hole in his logic and that he is perhaps not being quite as methodical and careful in the conclusions he draws from the cogito. The starting point is, of course, the projection of thought – the actual act of thinking and the way in which it defines and characterizes the human mind. To be as meticulous and scrupulous as Descartes himself (previously), how do we know that thoughts are, in fact, a projection of the human mind? How can it be known whether or not a thought is projected from who-knows-where and that it is the actual nature or essence of the mind to simply “tune in” to such projections or thoughts? If this, or some other phenomena, is indeed the case, then the conclusion established