What we know is that reason is extremely useful when applied to mechanical/material subjects. We should continue to use it in that way.

We know that it has extreme difficulty in explaining and analyzing some key issues, including consciousness and all of its manifestations; pain/pleasure, emotions, imagination, and meaning in general as well as others. Once again, this seems to be the case because consciousness itself is extremely difficult to put into mechanical/material terms. Therefore reason has a problem with it.

If a tool is proficient in explaining some things but not other things, is it 'rational' to consider it a universal tool? In this way I am using reason itself to conclude that it is not a universal tool.

So your question is what then should we use to understand consciousness if not reason?

Just as reason seems to do well in understanding things of a certain nature (mechanical/physical), we can look at consciousness and conclude from its mysteries what kind of tool is needed to give us insight into it.

(Notice that I am still using reason throughout this process, it never really leaves our endeavors. We are just being honest in that we recognize something more is there that is beyond its limits.)

Consciousness does not seem to be mechanical or physical in nature because we are not able to even model in theory an explanation for it. Therefore the tool to be used to understand it should have a much more mysterious/abstract nature. Once we make that conclusion it is a whole other topic as to what that other 'tool' might be. Whatever it is, it will probably be more elusive and less universally apparent throughout the human population than reason is.