Also, in this situation, would he be allowed to count what he pays to us as a Housing Allowance (clergy) expense?
If he is clergy AND If his congregation has designated in advance a portion of his compensation as housing allowance, THEN, yes, it seems to me that he could count the rent payments to you as housing expenses. I'd urge caution in record keeping - meaning be sure he writes you a check and puts on the memo "rent" since this is a family member situation. Be sure he pays all rent as agreed. (I am not a tax professional) I think he would be limited in other expenses since you as landlord do all the repairs and likely pay the utilities too. I suppose if he paints the rooms that are his he could count that expense or if he has a separate telephone line for himself.
hope this is helpful to you.