jdybnis
x86 is a convoluted horror. A lot of it makes no sense except in the context of backwards compatibility, which the documentation won't necessarily point out. I highly recommend picking up a microcontroller to learn on instead of a microprocessor. Microcontrollers are mostly self-contained systems, while microprocessors are just a small piece of the picture and have complicated interfaces to the rest of the system components.
I recommend picking something in the Freescale 68HC* family. The addressing modes and instruction set are fairly clean and the architecture is simple. Something based on ARM would probably also be straightforward to learn. Don't worry about choosing a 32 bit chip, 8 or 16 bit is fine. 8 and 16 bit chips are typically simpler and will still teach you the important concepts.
Spend a couple of weeks on this and your understanding of C will be easier to come by and more thorough.