Does anyone know what exactly Stallman means by 'functional part'? I would have assumed it to mean something like one feature, or perhaps one procedure, but that does not quite add up with his examples having two to three times as many 'functional parts' as they have lines of code.

If you read the paragraph that referenced it, it appears he's referring to constructs like 'if' statements and 'while' loops. In particular, he was contrasting the difference between mechanical engineering and software engineering:

> If I wanted to put an ‘If’ statement in a ‘While’ statement, I don't have to worry about whether the ‘If’ statement will oscillate at a certain frequency and rub against the ‘While’ statement and eventually they will fracture. I don't have to worry whether it will oscillate at a certain higher frequency and induce a signal in the value of some other variable. [...]