I started a small project of changing some bad pulleys and a by pass a/c pulley. While get everything situated and starting to take the tires off. I found the lug nuts extremely tight to the point of having to stand on a breaker bar to get them loose. I just had some new tires installed ,an alignment done and some new brakes. Since then I've noticed the brakes pulsating really bad. He did say he had to turn the rotors quite a bit and it might lead to warpage. So what all damage could the over tightened lug nuts have done ? I also bought new EBC rotors and pads. Just wondering about the hubs and if they are damaged (warped).

Chances are just the rotors were warped. I had to change mine for the same reason. Over tightening the lug nuts wont warp things nearly as much as torquing them uneven.

One of the issues I had was a bad wheel hub, which resulted in a warped front rotor. check the hubs before you install the rotors. You may need to replace one or both.

Is there an easy way to tell if the hubs are warped. Maybe a dial indicator and spin the hub?

The hubs should make no noise while rolling and you should have no wobble or play in them from top to bottom or left to right.

Don't forget the rust build up between the hub-rotor-rim assembly. This is especially worst if you live in salty places!

Using an impact to tighten a wheel is a no-no. Use torque sticks, or a torque wrench. Some anti-sieze on the rim hub, and the threads helps too. Removing the wheel frequently also keeps the nuts from siezing to as well.

Another thing to remember, if the back brakes are not adjusted properly, the front brakes are toast. I find I have to adjust my back brakes every 2-3 months, these drums are terrible for that sometimes.