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Well there's your problem.
You do realize that chimpanzees are genetically much closer to us than any aliens could possibly be, don't you?
Except by some amazing (read: impossible) fluke, you could substitute any known life form for "chimpanzees" in the above sentence.
There was no war...
I think you mean: "We have always been at war with East Asia"
We know that the Egyptians were really good at keepin records. Like "small family of farmers came in to Egypt to get some grain" kind of good records. And yet, there is no mention of 1000's of Hebrew slaves existing in Egypt, let along escaping, let alone the plagues that were supposedly brought upon the pharaoh, let alone the parting of the sea and murder of 100's (or maybe 1000's) of soldiers when the sea collapsed.
And then there's the lack of archaeological evidence of a large group of people "wandering" the deserts for 40 years.
The Evolution of Sexual Reproduction is another complex subject, but you can read about it at the link above. I beleive that the advantage of sexual reproduction was that when you swap genes, you can adapt faster (more possiblity for a bad transfer, more combinations of genes etc). The first sexual reproducers were probably hermaphrodites like flowers, fertilising each other with the wind (before insects). And that eventually developed into male and female genders. The other things that you mention are all explainable in a plausible way (see argument from personal incredulity).
This also allowed the total population in that group to explode (there's now more food in total, glucose + citrate).
Another cool thing is that this smashes the "Irreducible Complexity" argument. The ability to metabolise citrate is developed by two separate mutations, which, on their own achieve nothing. Some of the populations developed the first mutation and some developed the second one, but none of them had previously developed both. This shows that the "preliminary" mutations were not harmful to the bacteria, so they just "hung around" until one of them was lucky enough to get the second mutation too.
Anyway, look up Lenski's work, I'm sure his papers (and those of his students/colleagues) are better at explaining it all than me...
an external population with which to mediate the process.
Mediate how exactly? They still can't contribute to the "gene pool" since there is no pool. Asexual reproduction involves no transferral of genes within a generation, only from parent to child.
would the group go through a smaller or greater number of mutations?
On average, for the same number of generations, they would go through the same number of mutations. (This is of course disregarding things that would directly damage DNA ("free radicals")). The only effect that having them "inbred" (you really need to see this), in a lab is that the researchers can monitor and control the whole process.
There was also no theoretical reason for monopoles _to_ exist.
I think the point the GP was making was that there was no reason that they couldn't exist...
As is also shown in the video, you still have a keyboard (look near the end), so shortcuts are still available. I wouldn't mind betting that most of those 300+ actions are performed via shortcut keys.