zmx: It could be a few things. The spots may have been aggravated by PE, as you suggest, and thus making the spots that were already there bigger and more prevalent.
The spots could have also been there all along (and at their current size) and you just recently noticed them because you have been spending more time with your penis as of late (because of PE). Or the spots could be completely unrelated to PE and could be some benign growth (I have several of these on my legs).
More likely, though, the spots are just a sign of you going at it a little too intense. I wouldn't worry too much about it. Do what Joe suggests and take a week off. See if anything changes. If not, restart and pay close attention to the spots.
Also, I found this on the web:
AnswerSPOT | Student Health Services