All scripture is to be understood literally
When the term are properly understood, all passages of the Bible should be taken both literally and spiritually. As the Catechism says:
According to an ancient tradition, one can distinguish between two senses of Scripture: the literal and the spiritual, the latter being subdivided into the allegorical, moral and anagogical senses. The profound concordance of the four senses guarantees all its richness to the living reading of Scripture in the Church. 
Properly understood, the literal sense
is the meaning conveyed by the words of Scripture and discovered by exegesis, following the rules of sound interpretation. 
And in indispensable because
All other senses of Sacred Scripture are based on the literal. 
Thus, the correct answer to the original question of "has the Catholic Church outlined specific Biblical passages which should not be taken literally?" is no, because ALL scripture should be taken literally.
Proper understanding of "literal" and guidelines for application
The "problem" arises from an improper understanding of what "literal" means. It does not mean "shut off your brain and take the words at face value regardless of context." (Commonly called a "literalistic" reading.) At places, such an interpretation would be absurd. Instead, one should:
be attentive to what the human authors truly wanted to affirm, and to what God wanted to reveal to us by their words. 
take into account the conditions of their time and culture, the literary genres in use at that time, and the modes of feeling, speaking and narrating then current. 
Sacred Scripture must be read and interpreted in the light of the same Spirit by whom it was written. 
For example, when a Biblical author uses a metaphor to describe something, taking it "literally" means recognizing the author is using a metaphor to convey truth, not describing the physical characteristics of the situation in view. Of course, no one would disagree with that. The difficulty arises when an author's intent is not readily apparent. To help decide how to view a particular passage, the Second Vatican Council came up with three guidelines, outlined in Der Verbnum as summarized by the Catechism as follows:
Be especially attentive "to the content and unity of the whole Scripture". Different as the books which compose it may be, Scripture is a unity by reason of the unity of God's plan, of which Christ Jesus is the center and heart, open since his Passover. 
Read the Scripture within "the living Tradition of the whole Church". According to a saying of the Fathers, Sacred Scripture is written principally in the Church's heart rather than in documents and records, for the Church carries in her Tradition the living memorial of God's Word, and it is the Holy Spirit who gives her the spiritual interpretation of the Scripture (". . . according to the spiritual meaning which the Spirit grants to the Church"). 
Be attentive to the analogy of faith. By "analogy of faith" we mean the coherence of the truths of faith among themselves and within the whole plan of Revelation. 
It is up to the interpreter to use these principles, guided by the Holy Spirit, to help the Church better understand the Bible. 
In practical terms, the first principle is that all scripture was be interpreted in the light of all other scripture. If a literalistic reading of a particular verse doesn't make sense in context or in light of other passages, the author must have not intended it to be read that way.
The second principle basically means, one should not rely exclusively on their own understanding, but instead read the Bible in light of the many great commentators that came before them. If the Church Fathers viewed a passage as being a story intended to convey truths, that is a strong indication it is not literalistic history.
The third principle refers to the official teachings and doctrines of the Church. Because the dogmas and creeds of the Church have been established by received apostolic teaching, through sacred Tradition, if an interpretation of a Bible passage seems to contradict such teaching, the interpretation is wrong.
Readings desiring more details on proper understanding of Catholic Bible interpretation should consult Der Verbnum and The Interpretation of the Bible in the Church. It is well beyond the scope of this answer to completely summarize these documents, but I will add a few quotes from the latter to give a more complete picture of how Biblical interpretation is understood within the Catholic Church.
The Church continually strives to better understand the scriptures - no interpretation is ever "set in stone:"
The study of the Bible is, as it were, the soul of theology, as the Second Vatican Council says, borrowing a phrase from Pope Leo XIII (Dei Verbum, 24). This study is never finished; each age must in its own way newly seek to understand the sacred books.
The Church understands that the Bible is the work of humans and believes apply critical methods to the text enhances our understanding of it:
Catholic exegesis does not claim any particular scientific method as its own. It recognizes that one of the aspects of biblical texts is that they are the work of human authors, who employed both their own capacities for expression and the means which their age and social context put at their disposal. Consequently Catholic exegesis freely makes use of the scientific methods and approaches which allow a better grasp of the meaning of texts in their linguistic, literary, socio-cultural, religious and historical contexts, while explaining them as well through studying their sources and attending to the personality of each author
However, Church history is also invaluable to understanding:
What characterizes Catholic exegesis is that it deliberately places itself within the living tradition of the church, whose first concern is fidelity to the revelation attested by the Bible... Catholic exegetes approach the biblical text with a pre-understanding which holds closely together modern scientific culture and the religious tradition emanating from Israel and from the early Christian community. Their interpretation stands thereby in continuity with a dynamic pattern of interpretation that is found within the Bible itself and continues in the life of the church.
As previously discussed, the literal sense is key, but must be properly understood. Correct literal understanding leads to correct spiritual understanding, "the meaning expressed by the biblical texts when read under the influence of the Holy Spirit."
The document reaches the following conclusions (among others) that are especially relevant the the original question:
the interpretation of the Bible should likewise involve an aspect of creativity; it ought also to confront new questions so as to respond to them out of the Bible.
Granted that tensions can exist in the relationship between various texts of sacred Scripture, interpretation must necessarily show a certain pluralism. No single interpretation can exhaust the meaning of the whole, which is a symphony of many voices.
the interpretation of sacred Scripture requires full participation on the part of exegetes in the life and faith of the believing community of their own time.
With these guidelines in mind, it should be clear why the Church does not release lists of passages that should be interpreted as "literal" or "non-literal" history, for example. The correct interpretation is a dependent both on the historical situation in which a passage was written and the current faith community. Because of its inspired nature, the scripture adapts to new situations and answers new questions the original authors could not have envisioned.
To ask whether there was a "literal Noah's Ark," for example, completely misses the point of the scripture according to the Catholic Church. The literal sense is the meaning conveyed by the story of Noah's Ark. Whether there once was a person named Noah is irrelevant and cannot be determined from the text. Both options are equally valid views as the "literalistic sense" is an invalid way to view the Bible.
To reiterate, all passages of the Bible should be understood literally in the sense the Church defines the word. The sense of the word the OP uses is considered an invalid interpretation method by the Church. Thus, it does not define whether passages should be understood as "literal" or not in this sense.