What happened to Clementine?

A children's version of the very American love song Oh My Darling Clementine caught my ear this morning.  If you don't know the tune, have a listen here.  The children's version leaves out a very telling section, ending after verse five, so I was left wondering, what really happened to Clementine?  And the more I read the lyrics I wondered, what is really going on here?

Here they are so you can follow along with my thoughts:

Oh My Darling Clementine
In a cavern, in a canyon,
Excavating for a mine,
Dwelt a miner, forty-niner
And his daughter - Clementine.

CHORUS:
Oh my Darling, Oh my Darling,
Oh my Darling Clementine.
Thou art lost and gone forever,
Dreadful sorry, Clementine.
Light she was and like a fairy,
And her shoes were number nine,
Herring boxes without topses
Sandals were for Clementine
Drove she ducklings to the water
Every morning just at nine,
Hit her foot against a splinter
Fell into the foaming brine.

Ruby lips above the water,
Blowing bubbles soft and fine,
But alas, I was no swimmer,
So I lost my Clementine

How I missed her! How I missed her!
How I missed my Clementine,
But I kissed her little sister,
And forgot my Clementine. (child's version ends here)
Then the miner, forty-niner,
Soon began to peak and pine,
Thought he oughter join his daughter,
Now he's with his Clementine.

In a churchyard near the canyon,
Where the myrtle doth entwine,
There grow roses and the posies,
Fertilized by Clementine.
In my dreams she still doth haunt me,
Robed in garments, soaked in brine;
Then she rises from the water
And I kiss my Clementine.

By definition, this song is a folk ballad (a relatively short narrative poem, written to be sung, with a simple and dramatic action; folk ballads are usually anonymous and the presentation impersonal, citation).  There are many like this in every country's history.  In writing this post, I got so bogged down in research that I ended up learning about Scottish ballads and varying blackface minstrel tunes...Craziness!  The Internet never ends!
 
My original intent was to point out who confused I was by the song.  What a mystery this left in my mind!  Who was Clementine?  Who was this man that so loved her he wrote a song, but loved her so little he consoled himself with her sister?  What actually happened to her and where?  (For a brief and incomplete history on the song, click here.)
 
My brain is barely on topic anymore, but what I was aiming for was this: how do you tie up your loose ends in your writing?  (Let's not even talk about the loose ends or hug jumps in this post!)  How do you make sure you have closed all the doors you want closed, leaving only the cracks you want to leave?  What is your process?
 
Sorry for not tying it up so well today.  This darn Internet and my restless brain!