You're always welcome so long as you remain civil
To be honest I don't know much about the mechanism. I found
this very old mailing list post, but there doesn't seem to be a lot about the actual mechanisms. I suggest you ask someone who knows a lot about recombination and DNA repair. My best guess is that a piece of a chromosome is accidentally broken off and then put back in the wrong place (there
are known ways of putting broken DNA back together, that much I remember from my biochemistry class last semester

).
Actually, morphological change isn't that mysterious. You can often track down morphological changes to specific mutations in specific genes or their regulatory regions. Genes that control development can affect various aspects of morphology relatively easily. Development is a wonderfully intricate network of interactions; each controlling where, when and in what amounts things (proteins, cell types, tissues, organs) are produced.
An example of simple genetic changes leading to visible morphological change is the pelvic spines of three-spine sticklebacks. Sticklebacks can reduce or regrow pelvic spines (in fact, the entire pelvis) by mutations in a gene called Pitx1. The gene is expressed in many different parts of a stickleback embryo, and a different "switch" corresponds to each body part. A mutation in one switch can increase, decrease or turn off the expression of the gene in a body part, and since Pitx1 controls other genes, the whole pathway producing, say, a pelvis, is affected. You can find little videos on stickleback spines and their genetic switches
here.
It has no function (I know of) - and that's why it can't be put down to intelligent design.
You seem to be confusing evidence for evolution with evidence for how some evolutionary events happened.
What we (including us biology people) usually mean by evolution on this forum includes several related ideas. Technically, "evolution" is simply a change in the genetic make-up of a population.
Descent with modification is basically this; and that's where the
specific changes that happened from some prehistoric ape to humans belong. A related idea is
common descent: really, if creatures are capable of descent with modification, couldn't they come from a common ancestor by that process?
Now, you can infer common descent without knowing the details of the modification. The fused chromosome tells us nothing about what makes us different from chimps (chromosome fusion didn't do anything to the functional part of the chromosomes) - it is only evidence that we once shared a common ancestor. Some genetic markers can tell you something about two people's relatedness but nothing about why one has curly hair and the other has straight hair. You need to look at functional genes (or once-functional
pseudogenes 
) to find that out.
What are those in humans and chimps? I don't know much about the specifics, but
these look exactly like what you are looking for.