I guess what my situation was that I could balance school and the application, or school and the prototype. While I had an urge to work on the prototype I always felt guilty because frankly the application has a deadline, the prototype does not. Actually after the application deadline I was able to get back to the prototype.

If you get an interview, unbalance school to get the prototype ready - 'don't worry be crappy' - for the interview.

Oh definitely. In fact I did that the last time I prototyped a site and not only was I not doing it for any investors, I had finals the same week.