Ignoring all other errors, we have the illusion of an internal conflict in this sentence. Both "that" and "each" seem to funcion as the subject for the verb "perform",
BUT in this sentence, "each" is not functioning as a pronoun. Some would argue it is functioning as an adjective modifying the relative pronoun "that", which is the subject of the relative clause. Others would argue it is functioning as an adverb modifying "perform". Either way, "each" is neither singular nor plural. See Each.
Verb: comprises [sic]
Prepositional phrase: of multiple binary programs
Relative clause: (referent programs) that each perform a single task
In an additional test, the sentence would make perfect sense without the word "each":
foo comprises of multiple binary programs that perform a single task.
Therefore, ignoring other errors, the correct verb form would be perform.
"foo comprises of multiple binary programs that each perform a
That may be awkward style and improper use of the word "comprise", but otherwise it is the correct grammar for "each".