I’m quiet new to Kryptos (I heard about it before, but only until I became aware that it is still an unsolved mystery a very short while ago, I started reading about it a little more) and have not much to do with cryptology in general, but something of the whole Kryptos concept including the background of Sanborn is stuck in my head at the moment, which is: waves!
Of course the sculpture itself is in a waveform and then there are several versions of waves: we have water and (electro)magnetism, we have light and with a little bit interpretation maybe even brain waves (from the lucid memory), we have a (backwards) ray in the text and of course a propagating wave at least to me is also quiet symbolic for messages and Kryptos itself. 
Why am I posting this in a comment about the question mark?
At least to me a wave is something that is not defined at one single position, but as a change of usually an amplitude in time and/or space.
So how about not looking at the individual letters, but at the change between the letters?
To me this would make sense for a few reasons:
1) (and this is why I thought of posting it here): when you look not at the individual letters, but changes between them: to code for 97 letters, you would need 97 “changes” which means not 97 but 98 characters.
1a) of course this leaves the problem of how a ? fits in there, which is a problem. Maybe “T is your position”, can help with that?” However we also still have a “interpret a t u” (which btw had me first think of the genetic code actually, where in the RNA a T from the DNA becomes a U – but that’s somehow another story/theorie)
2) the amount of double letters could make more sense, because a change of “0″ could refer to a letter that is more common.
3) not knowing much about cryptology myself I at least asume and think this would “mask” the english language as JS described it as the frequency and distribution of letters will change.
Then of course there are still tons of follow-up questions: do we take the “normal” alphabet or the “kryptos-version” on the right side. Do we have “negative” and “positive” changes or does the alphabet go in “circles”?
I find this idea quiet intriguing, so I thought I’d somehow get it “out there”. Maybe something like this has already been tried or maybe someone that is more skilled in cryptology has an idea to go on from there.
Well, that turned out to be longer than intended. Hope anyone finds it at least remotly interesting.