You have a really lofty goal and I applaud your dreams. Building a basic e-commerce site is a challenge in and of itself; you might be better off building a wordpress site with an ecommerce plugin like opencart, marketpress or shopify. They do a lot of the work already for you.
Here are some of the major areas you'll need to consider:
- user authentication
- inventory (and how to 'reserve' items, for instance if you have 3 in stock and 4 people all try and add to cart at the same time...)
- adding items to cart
- sales / coupons / discounts
- template + layout. Creating individual php files for every screen will make you crazy, and isn't very URL/SEO friendly. You'll likely want to look into a great framework such as Symfony, CakePHP, ZEND, Yii, or Laravel
- contacting users; notifications
there are probably several areas I'm leaving out, but don't make the classic new developer mistake that if you don't build all of it by hand, it isn't legit. A lot of very talented people have already encountered a lot of real world problems and built great solutions to those--it isn't cheating to build off of their success.