I have created a form, however, I need to have certain lines calculate.

For example, there are 57 questions on the form. Questions 1, 20 & 39 should provide a score. Lines 2, 21 and 40 a score, etc. I would like the scores to be sent in a follow-up email once the survey has been completed. with all of the identifying information, name, email, ministry, etc.

It is possible to assign calculation values to your options:

http://www.jotform.com/help/301-How-to-Assign-Calculation-Value

Then total those up or perform further calculations using a calculation field:

https://www.jotform.com/help/259-How-to-Perform-Calculation-in-the-Form

Add a calculation field for each section you would like to score. 

These are our guides on setting up email notifications.  The first is on setting up notifications sent to you:

http://www.jotform.com/help/25-Setting-Up-Email-Notifications

The second is how to setup notifications to your users:

http://www.jotform.com/help/26-Creating-a-Form-Autoresponder