The Holy Modal Rounders did Junco Partner on their double album "The Holy Modal Rounders" about 1972 I think, which incorporates some variations of the above lyrics, eg

Down the road down the road down the road
Come a junco partner partner partner
He was loaded
As can be
He was knocked out
Knocked out loaded
He was loaded
With misery

Once I had
One million dollars
Had a lot of good friends
All around
Now I don't have
Any money
And my best friend's
A gonna put me down


(Repeat first verse)

There might be another verse but this song is fairly short (as are most of the songs on this excellent album).

The only "Junco" I have heard of is a Slate-coloured Junco (bird, possibly American). I would hazard a guess that it might mean the same thing as "Junkie", and that knocked out or loaded would mean under the influence of drugs. Anyway I suspect this is either a traditional song or one which long pre-dates Dr. John.