I went through it again, and found something else online about changing the folder to the root on godaddy. I did that, waited a few minutes and now when I go to site2.com, the address bar shows site1.com/site2, not site2.com. I think I'm missing an additional step so that site2.com shows up in the address bar?
Nevermind, I got it now, you have to check the box that says Primary, which is misleading because primary makes you think of the root domain, but it's working now.