"Thus, our thoughts are not automatically irrational just because they might be the result of natural occurances."
Assuming you are correct (and I think you are not), you would still not have any reason to believe that they are rational. Likewise, you would be in principle not even able to make a determination that X or Y is rational or irrational -- it would be decided for you by chance and nature. If you assume that some people are rational and others are irrational, you would have to say that those who are rational or irrational have (a) no control in whether they are rational or irrational, and (b) no control in whether you think they are rational or irrational. Which means that any determination of "rational" and "irrational" is ultimately meaningless, because we don't have control of either being rational or detecting it.