A 2-D kinetic Monte Carlo mesoscale model of molecular resists is developed to probe the effects of photoacid (PAG) homogeneity, specifically PAG aggregation behavior, on the resolution, sensitivity, and line-edge roughness (LER) performance of resists. The model reproduces many pattern defects that are commonly found experimentally by simply increasing the amount of PAG aggregation. The sensitivity of resists is found to change with increasing PAG aggregation in resists with low photoacid diffusivity, but remains near constant for resists with high photoacid diffusivity. Likewise, LER is found to increase with increasing PAG aggregation in resists with low photoacid diffusivity, but appears to be weakly dependent on PAG aggregation when the resist has high photoacid diffusivity. Increasing PAG aggregation limits the absolute resolution of a resist, because there exists a trade-off between the ability of photoacid diffusion to smooth out the inhomogeneity due to PAG aggregation and the blurring of the patterned feature that reduces resolution. Even very low levels of PAG aggregation appear to greatly limit the potential of a resist for sub- resolution patterning, but increased PAG loading appears to provide a way to mitigate this problem and allow for improved absolute resolution, even in the presence of aggregation.