We present a numerical modeling and simulation paradigm for multidomain, multiphysics systems with components modeled both in a lumped and distributed manner. The lumped components are modeled with a system of differential-algebraic equations (DAEs), whereas the possibly nonlinear distributed components that may belong to different physical domains are modeled using partial differential equations (PDEs) with associated boundary conditions. We address a comprehensive suite of problems for nonlinear coupled DAE-PDE systems including 1) transient simulation; 2) periodic steady-state (PSS) analysis formulated as a mixed boundary value problem that is solved with a hierarchical spectral collocation technique based on a joint Fourier-Chebyshev representation, for both forced and autonomous systems; 3) Floquet theory and analysis for coupled linear periodically time-varying DAE-PDE systems; 4) phase noise analysis for multidomain oscillators; and 5) efficient parameter sweeps for PSS and noise analyses based on first-order and pseudo-arclength continuation schemes. All of these techniques, implemented in a prototype simulator, are applied to a substantial case study: a multidomain feedback oscillator composed of distributed and lumped components in two physical domains, namely, a nano-mechanical beam resonator operating in the nonlinear regime, an electrical delay line, an electronic amplifier and a sensor-actuator for the transduction between the two physical domains.