Do you still withhold some payment for the job? If you do, don't pay the contractor the remaining fund.
The lien is bs. Did the contractor ask you to sign a pre-lien agreement? If not, he can't even file a lien against your property.
The problem of the roof you described has nothing to do with the temperature. It is bad workmanship. More like the felt-the black paper was not laid properly.
The nail pops are more likely the result of the nails are not nailed on the stud.
Bottom line- don't pay any more until he corrects the problems.
Try to document all your communication with him, just in case you them later. Written documents are better than your word & his word.
By the way, these rednecks like to take advantage of immigrants who do not speak English well.