I agree with Kathryn. Mushin does not have to be a deep trance, but is rooted in the here and now. And whether it is a temporary state or not doesn't really matter. After all, sleep is a temporary state, and being asleep all the time is akin to being in a coma, but that doesn't mean we shouldn't sleep everyday.
Takuan's work* is particularly relevant to martial artists; it was written for martial artists. The idea is not to become fixated on any one thought. That's not the same as "not having any thoughts". It is difficult to explain in words, but try some meditation and worry less about the anatomical side of things. I started out the same way (I'm a scientist by trade), but at some point you just have to sit and try it.
Best of luck!
*An excellent summary is in Minoru Kiyota's book "Kendo: its philosophy, history and means to personal growth" (1995). I've read the translation of Takuan's original essays, and it's really hard work to read! :-)