<p>iCalculus, you really don’t get it, as you say. Berkeley is, like Stanford, entirely superior to Harvard for engineering. And while I almost never call out other posters as ■■■■■■, you do seem inclined to groundless, inconsistent posts.</p>
<p>OP, Pea is right that transferring into Stanford is an extreme long shot these days, and with your GPA that is probably even more true in your case. I don’t know that Caltech or Mudd would take a close look either with your current GPA, though you might be able to point out that you received inadequate/poor advising at Harvard–it sure sounds like it. 
Maybe you can get some better advising, show a sharp upward trend in grades during the next term, and then consider transferring? I hope everything turns out well for you.</p>