Known as ponderingman on YouTube, this Kryptos new-comer suggests that the raised letters YA and R are markers referring to the plaintext characters in those same positions.
Those letters would be WL and D from the following:
Furthermore, he suggests a reason for the misspelling of DESPERATELY. By removing the W, L, and D (raised letters) from the plaintext, we get a possible new keyword, if somewhat out of order:
Jim’s talks about standing waves and layers gives this idea some credence.