Nanotyrranous may or may not be a real species of dinosaur. There are only two confirmed specimens known to exist, which indicates that it might just be a juvenile example of a tyrannosaur rather than an entire species unto itself.
Throughout the episode Holmes is continually trying to work on using a cordless drill on a human skull. This is a procedure called 'trepanation', by which burr-holes are drilled into a person's skull. This is conducted medically to relieve pressure caused by internal bleeding around the brain, but historically it was also used to 'release the evil humors' as Holmes offers to do for Watson at the end of the episode. This was meant to 'save' someone from madness or demon possession.
The title is an allusion to the phrase "dead man walking," which means a condemned prisoner walking to the death chamber, or someone who is doomed to die. The fossilized species was historically doomed to extinction.
A clade is a group of organisms that consists of a common ancestor and all its lineal descendants. These would more commonly be represented in a single branch on the "tree of life". The "common ancestor" could be an individual, a population, even a species, and so on.
Eating paper is a very bad idea as the human stomach cannot digest it. If enough paper is consumed it can get lodged in the intestines causing a bowel obstruction which would have to be surgically removed.