*** UPDATE *** After a lot of headscratching and pondering book 2 was found by Joseph TavanoI have updated the clue information below to show how I think it's location was worked out.
We are off again, this time the search area is Boston.@MyTheseus has suggested that this might point to the City of Squares in Boston otherwise known as Cambridge
Second clue
Third clue.Picture of Blaise de Vigenère which leads us to the Vigenère cipher to decode the letters in the second clue, using Monkey as the keyword gives us - "Home of the engineers"
Clue fourPossibly relating to Wavy Gravy the Hippie Clown
If you rake WAVY GRAVY and reverse it it to GRAVY WAVY, spend the two 5's i.e. remove the roman numeral number 5 (V's) from the name you get GRAY WAY which is a street on the MIT campus.

The L. in this clue refers to building 50 (Roman numeral again).So looking at the map above the building is the Walker Memorial building.
Possibly relating to the Castor Genus of Beaver, as the Engineers team mascot is Tim the BeaverConfirmed, just inside the building is a mosaic of Tim the Beaver.
A poem by Ogden NashThe full poem is -
A flea and a fly in a flue
Were imprisoned, so what could they do?
Said the fly, "let us flee!"
"Let us fly!" said the flea.
So they flew through a flaw in the flue.
The book was hidden in an old Flue just inside the building.
