I think you're in a really good place to get into a top school. In my experience, if you've already had skype interviews you've got a really good chance of getting an in-person official interview. If you get one of those you've got like a 75% chance of getting in. Also, keep in mind that Skype interviews are offered all the way out to January depending on the professor, so you might still hear from the other two proffs. I will also say that I had 0 publication when I applied and I got into two Ph.D. programs and got offers to masters programs from 2 others. I also didn't have nearly as much research experience as you and was coming straight from undergrad. You'll be ok.