  We simulate the 3+1 D classical Yang-Mills dynamics of the collisions of
longitudinally extended nuclei, described by eikonal color charges in the Color
Glass Condensate framework. By varying the longitudinal thickness of the
colliding nuclei, we discuss the violations of boost invariance and explore how
the boost invariant high-energy limit is approached. Subsequently, we develop a
more realistic model of the three dimensional color charge distributions that
connects longitudinal and transverse fluctuations to the $x$ and $k_\bot$
dependence of transverse momentum dependent parton distributions, and explore
the resulting rapidity profiles and their longitudinal fluctuations.
