Loose Lug Nuts - Torqued - Still making clunking sound?

You're right, but not warped. Once the wheel was driven on while loose, the holes and lug nuts become chewed up, then the carefully-machined friction surfaces no longer match. The only solution is to replace the wheel and the lug nuts. No matter how tight you make the lug nuts now, they will always work loose again.

As Doc said, the mounting holes in the rim will have been damaged from the pounding. The Wheel, lug nuts and likely the lug studs all need to be replaced in order to repair it. The wheel because the lug nut holes and seats are damaged as is the pilot surface on the rear of the wheel. The lug nuts because of the hammering from being loose enough to move and the lug studs because of thread damage and very possibly stress damage from the motion on them as the wheel moved. I have seen lug studs snap off after being reused in these situations, usually while the vehicle was in motion.