I found the guy's name who wrote the revised lyrics in one place - Major Robert P. Knoph - and this version of the song, which did not list the author's name, in another. I suppose Knoph is the culprit:

Puff the Magic Dragon

Puff the Magic Dragon, a bird of Cam Ranh bon
Came to fly the evening skies
In a land called Vietnam.

Puff the Magic Dragon, came across the sea,
To write it's name in guns of flame
In the heart of hostile SEA

When the grunts are in trouble
And Charlie's all around
The thoughts may pry into the sky
Beneath the fires on the ground

The VC's mortal terror, starts when many cries
And the Dragon's breath of sudden death
Comes screaming from the sky.

Yes, Puff will still be flying,
From one corps down to four
Till Charlie's gone and the evening comes
It's like the year before.

But I'll remember always, the ground troops grateful cry,
When fire is beamed and Charlie screamed
At the Dragon in the sky.

Now Dragons live forever and the Puff is just the same,
The Gooney Bird will still be heard when Grandpa is my name.
It will have to roam the skies with friends ..not with me
For I'm going home, no more to roam
In a land across the sea.

Puff the Magic Dragon, a bird of Cam Ranh bon
Came to fly the evening skies
In a land called Vietnam.

Puff the Magic Dragon, came across the sea,
To write it's name in guns of flame
In the heart of hostile SEA