I'm replying too late, but:
You are faced with several problems if you want to create superfamilies or trace their history back to a single language.
At first, I'm not a linguist,just interested in languages and phonology so I wouldn't create superfamilies. Atleast, very good understanding of grammar would be needed.
Yes, there are some problems for making superfamilies and first language reconstruction. But, I think, common problems for superfamilies or first language is what makes superfamily or first language reconstruction interesting.
No one knows when humans first started speaking, but assuming conservatively it was 50,000 years ago
Reconstructed Proto-Human or Proto-World (not fully recostructed) hypothesized to have been spoken between 100,000 and 200,000 years ago. Atleast this is what Wikipedia are saying.
that is a very long time when you look at how rapidly languages can change.
The Norman Conquest is what makes the English language rapidly changing.
and even then there are uncertainties about how to interpret ancient texts, especially those not written with alphabetic or syllabic scripts.
This is proto-writing. Examples of proto-writing are Vinča symbols and Jiahu symbols.
If two proto-languages share a lexeme how can you know whether it is because one borrowed from the other or because they had a common ancestor?
Yes, this is true. If two proto-languages have something common, we cannot know if this something common are borrowed or not. Indo-Uralic hypothesis is great example of this. In my opinion, Proto-Indo-European and Proto-Uralic are probably descsended from Proto-Indo-Uralic, because this is where is the point of superfamilies.
if the word in proto-language A for "rope" corresponds with the word in proto-language B for "snake" it may or may not be significant.
It may be significant, because similar appearance is what causes rope and snake to be easily confused. With this confusion, snake can be easily interpreted as moving rope. If the words of rope and snake are similar, it can cause even more confusion.
If you consider that within Indo-European there is no agreement about how Slavic and Baltic relate to each other you are not going to get agreement about how proto-languages relate to each other.
In my opinion, most linguists think that Baltic and Slavic related to each other and descended from Proto-Balto-Slavic language.
The reconstuction of the first language is a chimera.
If the reconstuction of the first language is a chimera, then most proto-languages would be chimera, probably because lack of writing. Even Proto-Indo-European. But there are really some people interested in proto-languages, or even first language. Or even proto-Human (Proto-World.) For these people, it's not even important whether proto-language is chimera or not, I think. For me, the most important part is that the proto-language is even reconstructed.