The relationships among charge order, spin fluctuations, and superconductivity in underdoped cuprates remain controversial. We use neutron scattering techniques to study these phenomena in La$_{1.93}$Sr$_{0.07}$CuO$_4$, a superconductor with a transition temperature of $T_c = 20$~K. At $Tll T_c$, we find incommensurate spin fluctuations with a quasielastic energy spectrum and no sign of a gap within the energy range from 0.2 to 15 meV. A weak elastic magnetic component grows below $sim10$~K, consistent with results from local probes. Regarding the atomic lattice, we have discovered unexpectedly strong fluctuations of the CuO$_6$ octahedra about Cu-O bonds, which are associated with inequivalent O sites within the CuO$_2$ planes. Furthermore, we observed a weak elastic $(3bar{3}0)$ superlattice peak that implies a reduced lattice symmetry. The presence of inequivalent O sites rationalizes various pieces of evidence for charge stripe order in underdoped lsco. The coexistence of superconductivity with quasi-static spin-stripe order suggests the presence of intertwined orders; however, the rotation of the stripe orientation away from the Cu-O bonds might be connected with evidence for a finite gap at the nodal points of the superconducting gap function.