Carl Scherzer used Ximénez’s heading as the title to his 1857 edition, but it was Charles Étienne Brasseur de Bourbourg who coined Popol Vuh in his 1861 edition. Brasseur also included an astounding 262-page prefatory “dissertation” which seems to have caused Brasseur’s edition yo be regarded as more authoritative. Furthermore, Brasseur concealed the fact that he possessed the Ayer manuscript in his library. After Brasseur’s death, the manuscript passed to Alphonse Pinart and then to Edward E. Ayer who donated it to The Newberry Library in 1911 where it was not (re)discovered until 1941. This long period of unavailability prevented anyone from ever correcting Brasseur’s arbitrary title and it has stuck ever since.
The phrase “Popol Vuh” is in the manuscript. Brasseur did not pull the phrase “Popol Vuh” out of thin air. It can be found in the third bicolumnar folio. Of course, the Quiché spelling differs and thus gives rise to the alternate modern spelling such as “Popol Wuj.”
“Popol Vuh” does not require a definite article. Even where it appears in the manuscript, “Popol Vuh” is not preceded by a definite article (and Brasseur did not use a definite article in his actual title but often did when writing about the text). Westerners have a tendency to elevate sacred texts through the use of definite articles, as is the case with The Bible, The Talmud, The Quran, The Bhagavad Gita, etc. Even though it seems more correct to Anglophone ears to use a definite article, it is perfectly acceptable and proper to omit a definite article.