In this work we use Lagrangian perturbation theory to analyze the harmonic space galaxy clustering signal of the Bright Galaxy Survey (BGS) and luminous red galaxies (LRGs) targeted by the dark energy spectroscopic instrument (DESI), combined with the galaxy-galaxy lensing signal measured around these galaxies using Dark Energy Survey Year 3 source galaxies. The BGS and LRG galaxies are extremely well characterized by DESI spectroscopy and, as a result, lens galaxy redshift uncertainty and photometric systematics contribute negligibly to the error budget of our "2×2-point"analysis. On the modeling side, this work represents the first application of the spinosaurus code, implementing an effective field theory model for galaxy intrinsic alignments, and we additionally introduce a new scheme (maiar) for marginalizing over the large uncertainties in the redshift evolution of the intrinsic alignment signal. Furthermore, this is the first application of a hybrid effective field theory model for galaxy bias based on the aemulus ν simulations. Our main result is a measurement of the amplitude of the lensing signal, S8=σ8(ωm/0.3)0.5=0.850-0.050+0.042, consistent with values of this parameter derived from the primary cosmic microwave background. This constraint is artificially improved by a factor of 51% if we assume a more standard, but restrictive parametrization for the redshift evolution and sample dependence of the intrinsic alignment signal, and 63% if we additionally assume the nonlinear alignment model. We show that when fixing the cosmological model to the best-fit values from Planck PR4 there is >5σ evidence for a deviation of the evolution of the intrinsic alignment signal from the functional form that is usually assumed in cosmic shear and galaxy-galaxy lensing studies.