So... did you understand the difference between a protein and the gene that codes for it? Did you understand how 2 genes can have 1 coding difference and still produce the exact same protein? Did you understand why Vade's statement re: human vs. chimp versions of the cytochrome c gene had 1 base pair difference, and Theobald's statement that the cytochrome c proteins themselves were exactly the same, are not contradicting each other?
Let me note one thing though - the total sequence of a protein is significant. If one cuts off or adds to a protein any length from either side functioning is changed.
Not true at all! The biggest paragraph in Theobald's article explained in detail that many, many, MANY substitutions were possible in the protein itself and it still worked just fine.
This is important, of course. This shows why your argument against gene duplications leading to new genes with new functions is just plain wrong.