I have read many websites and even shops specifically for the hobby. I was wondering if any of my arduino buddies know a good site that takes you through the process of building and programming a quadcopter from scratch? I am looking to do this piece by piece. Thank you for your help!
Check out this video:
building and programming a quadcopter from scratch
If you mean you want to design the electronics and write the flight control software from scratch, that's a huge job and you could literally spend decades figuring out how to do it yourself from scratch. If you're going to be more sensible and adopt a known working flight controller then there seems to be several open source ones to choose from and support forums associated with them where you can get guidance on how to implement your own project.