The Zen of the samurai was quite simple, unrefined, & direct. Sit strongly & alert with shoulders relaxed letting the breath sink down & expand by itself until the mind empties & "all this" appears just as it is.
In the Zen state of calm stillness mind & body naturally unify (they were never "two"), intellectual problems disappear, & the luminousness of reality shines forth.
If one has difficulty stopping thoughts (the experience of mental agitation, in its many forms), one can count to ten, putting one-pointed mental focus on each number in turn & using quiet force to sink breathing into the Hara.
One can also use a small bell, ringing it & listening to the reverberations die away, or gaze at the flame of a candle as a way of stopping thinking (Mokuso).
In a calm & delightful state of pure alertness, what need do you have of "thoughts" anyway?