To better model the efficient production of cosmic rays (CRs) in supernova remnants (SNRs) with the associated coupling between CR production and SNR dynamics, we have generalized an existing cr-hydro-NEI code (i.e., Ellison et al. 2012) to include the following processes: (1) an explicit calculation of the upstream precursor structure including the position dependent flow speed, density, temperature, and magnetic field strength; (2) a momentum and space dependent CR diffusion coefficient; (3) an explicit calculation of magnetic field amplification (MFA); (4) calculation of the maximum CR momentum using the amplified magnetic field; (5) a finite Alfven speed for the particle scattering centers; and (6) the ability to accelerate a superthermal seed population of CRs as well as the ambient thermal plasma. While a great deal of work has been done modeling SNRs, most work has concentrated on either the continuum emission from relativistic electrons or ions, or the thermal emission from the shock heated plasma. Our generalized code combines these elements and describes the interplay between CR production and SNR evolution, including the nonlinear coupling of efficient diffusive shock acceleration (DSA), based mainly on the work of P. Blasi and co-workers, and a non-equilibrium ionization (NEI) calculation of thermal X-ray line emission. We believe our generalized model will provide a consistent modeling platform for SNRs, including those interacting with molecular clouds, and improve the interpretation of current and future observations, including the high-quality spectra expected from Astro-H. SNR RX J1713.7-3946 is modeled as an example.