Rozemarijn,
1) A mask is useful for two reasons: (a) to hide the stuff outside the brain, and (b) provide FDR q-values in the output that would be unnecessarily penalized for the voxels outside the brain.
2) The alpha level would be only available on the cluster report table if you perform the population-level analysis with 3dttest++. In your case with 3dLME, you have already decided the alpha threshold (presumably 0.05) through 3dClustSim. In other words, once you provide the cluster size threshold on the AFNI, all the surviving clusters would have an alpha level of 0.05 or less.
Gang
