My apologies, I thought I answered this question when I stated the following "The bottom bracket will thread into the shell perfectly smooth without any clicks or grinding." And yes, I have have tightened both cups to the recommended torque specifications without any problems. If that does not answer your question what exactly would I be searching for to determine if there is "thread skip" or "stripping"?

Two nights ago I installed a friend's crankset, BB, and pedals that he had laying around. The noise disappeared for about 3 miles and then slowly came back with a vengeance. This leads me to believe that even if the threads are in good shape there is just too much play in the BB and the creaking is coming from where the BB meets the BB shell.

I appreciate all of the help that I received. Thanks guys!