The question has basically been answered via the comments but it may help to summarize the conclusion.  If you insist that the input be <i>unclocked</i> NP machines then nothing useful can possibly be computed from the input, as explained in the answer to <a href="https://mathoverflow.net/questions/28056/given-a-polynomial-time-algorithm-can-we-compute-an-explicit-polynomial-time-bou/28060#28060">this related MO question by Joel David Hamkins</a>.  But this kind of uncomputability result is, I would argue, completely uninteresting and irrelevant to your intended question, because it has <i>absolutely nothing at all to do with P or NP</i>.  It just amounts to the fact that arbitrary Turing machines are intractable objects.  On the other hand, if the input is a <i>clocked</i> NP machine, then Cook's reduction shows how to construct a P machine that solves your problem (assuming P = NP).  This is really what we care about in practice.  If I have a problem that I know is in NP, then I want a mechanical way of producing a polytime algorithm for it (assuming P = NP).  It's really irrelevant that there are all kinds of other, bizarre NP machines that accept the same language, and that it's an uncomputable task to sift through them.