Background: Establishing computationally tractable models of atomic nuclei is a long-time goal of nuclear structure physics. A flexible framework which easily includes excited states and many-body correlations is the configuration-interaction shell model (SM), but the exponential growth of the basis means one needs an efficient truncation scheme, ideally one that includes both deformation and pairing correlations.Purpose: We propose an efficient truncation scheme of the SM: starting from a pair condensate variationally defined by Hartree-Fock single-particle states and the particle-number conserved Bardeen-Cooper-Schrieffer (NBCS) approximation, we carry out projection of states with good angular momentum.Methods: After generating Hartree-Fock single-particle states with Kramers degeneracy in a SM space, we optimize the pair amplitudes in the NBCS by minimizing the energy, and then use linear algebra projection (LAP) of states with good angular momentum. Both NBCS and LAP are computationally fast.Results: Our calculations yield good agreement with full configuration-interaction SM calculations for low-lying states of transitional and rotational nuclei with axially symmetric and triaxial deformation in medium- and heavy-mass regions: $^{44,46,48}\mathrm{Ti}$, $^{48,50}\mathrm{Cr}$, $^{52}\mathrm{Fe}$, $^{60,62,64}\mathrm{Zn}$, $^{66,68}\mathrm{Ge}$, $^{68}\mathrm{Se}$, and $^{108,110}\mathrm{Xe}$. We predict low-lying states of $^{112--114}\mathrm{Ba}$ and $^{116--120}\mathrm{Ce}$, nuclei difficult to reach by large-scale SM calculations.Conclusions: Both pair correlation and the configuration mixing between different intrinsic states play a key role in reproducing collectivity and shape coexistence, demonstrating the utility of this truncation scheme of the SM to study transitional and deformed nuclei.