Let $k$ be an algebraically closed field of positive characteristic $p$. We first classify the $D$-truncations mod $p$ of Shimura $F$-crystals over $k$ and then we study stratifications defined by inner isomorphism classes of these $D$-truncations. This generalizes previous works of Kraft, Ekedahl, Oort, Moonen, and Wedhorn. As a main tool we introduce and study Bruhat $F$-decompositions; they generalize the combined form of Steinberg theorem and of classical Bruhat decompositions for reductive groups over $k$.