That's an interesting idea... it would explain a lot of things, but genes don't really work like that.
If it was true that our closer ancestors were nocturnal, we could have developed some nocturnal characteristics... but that would probably have to have been a relatively very short period of evolution, with only a few "major" genes being introduced. Of course we have had nocturnal ancestors in the remote past, but our recent ancestors and closest great ape cousins are designed to be most efficient in the daylight. It is possible that for a time, hominids moved about and scavenged after sunset because it was safer, as a cultural adaptation, and some genes were brought forward for better night-time sensitivity in an isolated population- but- as a whole, humans are and have been for quite some time diurnal. And the human genome, on a whole, is very similar.
And because the average person has a very mixed genetic heritige, it is highly unlikely genes selected for nocturnal life in the recent past would recombine in any one individual, and certainly not at the rate that Aspergers presents itself.... because there is no gene responsible for being nocturnal, it is a large number of genes that are randomly distributed throughout the population, and becoming nocturnal takes a lot of "evolving".
You don't inherit certain traits, you inherit genes that work with other genes to create traits.
Once a certain gene has been introduced into a population of new genes, the genes work together to create characteristics in different ways, depending on the type of gene.
That is why we don't spontaneously sproud a tail, or scales, even though we may still have the same "genes" for fur and scales as our ancestors did.
Asperger's is likely genetic in nature, which means it can run in families, but when you're talking about ancestors that distant, than the heritability no longer really applies on that level, since such a larger percentage of the current population would share the same genes, and then many more people would also share the same characteristics.
A more suitable explanation for the high rate of sleep problems would be one that accounts for sensitivity issues and higher stress levels impacting hormone regulation.
It is a nice theory though! But its just very very unlikely that there would be such a straightforward genetic answer such as that one... 