A direct numerical simulation of many interacting ions in a Penning trap with a rotating wall is presented. The ion dynamics is modeled classically. Both axial and planar Doppler laser cooling processes are modeled using stochastic momentum impulses based on two-level atomic scattering rates. The plasmas being modeled are ultracold two-dimensional crystals made up of hundreds of ions. We compare Doppler cooled results directly to a previous linear eigenmodes analysis. Agreement in both frequency and mode structure is obtained. Additionally, when Doppler laser cooling is applied, the laser cooled steady state plasma axial temperature agrees with the Doppler cooling limit. Numerical simulations using the approach described and benchmarked here will provide insights into the dynamics of large trapped-ion crystals, improving their performance as a platform for quantum simulation and sensing.