If you didn't actually work with your pastor, then don't send that letter. The only school that I know of that takes letters from clergy and seriously looks at them as a "personal reference" is Loma Linda. It might even look bad, because schools can interpret that as a sign that you weren't able to get people that you worked with to write letters for you. However, if you did actually work with the pastor (ie: you worked closely with him/her as a youth group leader, or along that lines), then a letter from your pastor would be perfectly fine.
Also, make sure that the school WILL accept more than 2 letters. Some schools are very strict about this, and will throw out any extra letters they receive. Otherwise I think 3 letters are fine, as long as they are strong letters. It's better to only send 3 strong letters rather than 3 strong and 2 weak letters, because the messages of the 3 you like would get "diluted" if you send 5.
Remember that you can also send in extra letters after you have already send in your original application. I would recommend sending in the 3 now with your secondary, then if there are any others you decide to send later, you can send them in when you want.
