Marc, "Crucifixion" is definitely about J.F.K.'s assassination. I've had it in my collection for many years. (The collection is now at the Archive Of Folk Culture at the Libr. of Congress. I started the collection---- SONGS OF THE LIFE, TIMES AND ASSASSINATION OF JOHN FITZGERALD KENNEDY-----way over 30 years ago.
The best version of "Crucifixion" was done by JIM & JEAN (Glover). Jim was a roomy of Phil Ochs's at Ohio State U. Ochs wrote several songs featuring JFK----not all on the assassination itself. One that was is "That Was The President and That Was The Man". Several were printed in BROADSIDE. Dylan's, Paxton's, many others had their early songs printed there.
And all the info that could be found via Mudcat on PAUL CLAYTON (WORTHINGTON) can be found at THAT THREAD! Have fun! (Info. his connections to Dylan's songs is talked about there too.) Art Thieme