Which state you live in?

Which state you live in?
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.