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Solid-state molecular qubits with open-shell ground states have great potential for addressability, scalability, and tunability, but understanding the fundamental limits of quantum coherence in these systems is challenging due to the complexity of the qubit environment. To address this, we develop a random Hamiltonian approach where the molecular g-tensor fluctuates due to classical lattice motion obtained from molecular dynamics simulations at constant temperature. Atomistic g-tensor fluctuations are used to construct Redfield quantum master equations that predict the relaxation T1 and dephasing T2 times of copper porphyrin qubits in a crystalline framework. Atomistic T1 predictions due to one-phonon spin-lattice interaction overestimate the available experimental data by orders of magnitude. Quantitative agreement with measurements at all magnetic fields is restored by introducing a magnetic field noise model to describe lattice nuclear spins, with field-dependent noise amplitude in the range δB ∼ 10 μT - 1 mT for the copper porphyrin system. We show that while T1 scales as 1/B experimentally due to a combination of spin-lattice and magnetic noise contributions, T2 scales strictly as 1/B2 due to low-frequency dephasing processes associated with magnetic field noise. Our work demonstrates the potential of dynamical methods for modeling the open quantum system dynamics of molecular spin qubits.