Why Don't We Find "Come Thou Fount" in the hymnbook?

Come, Thou Fount of Every Blessing

This is a favorite hymn of missionaries world-wide and for those in the Ghana MTC, they are not an exception.  Before the current hymnal was published, "Come, Thou Fount of Every Blessing" was a little-known hymn. The 1985 hymnbook committee elected to remove it from the new hymnal in favor of other works because so few members knew the song. 

However, after the revised hymnal was published, Mack Wilberg wrote an iconic arrangement of the hymn, bringing it into the forefront of members' minds. Today, due to its renewed popularity, many members still question why the hymn was ever removed as it is now one of the most beloved LDS songs not in the official Church hymnal.  (And to quote Paul Harvey....that is the rest of the story.)

HYMNS FUN FACT: Over 6,000 submissions of texts and tunes were reviewed for the 1985 hymnal.

Source:  http://www.ldsliving.com/story/76560-10-things-you-didnt-know-about-your-favorite-lds-hymns

And....what about the phrase in the second verse that says "here I raise my Ebenezer?

In 1 Samuel 7, the prophet Samuel and the Israelites found themselves under attack by the Phillistines. Fearing for their lives, the people begged Samuel to pray for the plight against the Philistines.  Samuel offered up a sacrifice to the Lord and prayed for His protection.  The Lord listened to Samuel and caused the Philisitines to lose the battle.  "Then Samuel took a stone and set it up between Mizpah and Shen, and call its ahem Ebenezer,, saying ;thus far the Lord has helped us.'" (v 12)

The word 'ebenezer' comes from the Hebrew words "stone of help."  An Ebenezer therefore is simply a monumental stone set up to symbolize the assistance the Lord gave the person raising the stone.