1) Just add several columns to the cart to account for all of the options.
2) If it doesn't follow a regular formula you would have to store all three or four or however many prices in that many separate columns. Then you can use a calculation to determine the correct price based on quantity.
3) You would want the SSL on the page with the form. You should never send credit card information in an email. If you need to store it in the database, you can use something like mcrypt() in php to encrypt the card number from a key for optimal security. Another option that isn't horrible is to only store the card number until it is used and then delete it. The last thing you want is a database with all of your customers credit card numbers over time. Reducing the length of time card numbers are stored and encryption are both good ways of minimizing the risk of storing credit cards.