Problem solved: I found the lyrics! Thank you anyway. It was a matter of doing the research the right way. After a series of attempts I googled "midnight special flapjacks molasses" and the first result was
this pdf file which is the booklet of the album "Folk Music of the Newport Folk Festival 1959-60, Vol. 2" published by the Smithsonian Folkways Records. Bang!
I think it is a good idea to transcribe the lyrics I found for the benefit of others interested in Terry & McGhee's rendition of this wonderful tune.


MIDNIGHT SPECIAL
Sung by Brownie McGhee and Sonny Terry

CHORUS:
Oh, let the Midnight Special
Shine her light on me.
Let the Midnight Special
Shine her ever-loving light on me.

Yonder comes Miss Rosie.
How in the world do you know?
Well, I know her by her apron
And the dress she wore;
Umbrella on her shoulder,
Piece of paper in her hand;
Well, she's gonna see the gov'nor
Just to 'lease her man.

(CHORUS)

Oh, when you get up in the morning
And the big bell rings
You go marching to the table,
Find the same old thing:
No forks on the table,
And nothing in your pan;
If you say anything about it,
You have trouble with the man.

(CHORUS)

If you ever go to Houston,
Boy, you better walk right,
Well you better not squabble,
And you better not fight.
That cop will arrest you,
He'll sure take you down.
You can bet your bottom dollar
You're jail-house bound.

(CHORUS)

When you get up in the morning
And the ding dong ring,
You go marching to the table,
Find the same old thing:
Flapjacks and molasses
And that sow-belly fat;
If you say anything about it,
Well, you won't get that.

(CHORUS)

I was standing at the station
When my baby got on board.
I was standing there begging,
"Baby, please don't go."
When that train was leaving,
Miss Rosie inside,
I couldn't do nothing,
Hang my head and cry.

(CHORUS)