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Spend 20 minutes talking to each other once or twice a week on Skype. By the time you have to make the video, you'll be pretty comfortable with it.

Also, close AIM/GTalk/Twitter/whatever while you do this. Don't let yourselves fall back to another way of talking to each other.

Skype works. Sometimes the sound is hard to deal with. However, consider that there are probably 20 other people in your same situation who will hack out a quick skype video.

Keep it simple don't overthink the stuff.

Do what you can. You won't be the only one using a skype call.

My Co founder and I had the same problems. The solution? Skype+Screenr :). It worked out fine.

Good luck in your application.