I would recommend looking at the course The Elements of Computing Systems. Most of the material you need to complete the course is online and the textbook is inexpensive (I paid about 50.00 USD for my copy).
The course takes you through constructing a basic computer system from the NAND gate on up. All of the labs are done in simulation software and it would not be a large stretch of the imagination to convert it to actual hardware (using VHDL).
There is also a Google Tech talk on the the course.
http://video.google.com/videoplay?docid=7654043762021156507
If you want to dive in deeper than digital electronics (logic gates) and learn about analog electronics (the transistors and other components that gates are constructed out of), and the physics behind electricity I recommend Teach Yourself Electricity and Electronics
