K1 and K2 are straightforward Vigenere ciphers that use the right hand side of the Kryptos Copperplate and the keywords “palimpsest” and “abscissa” respectively.
But what about K3?
Here’s one method and a site that will make it easy to see for yourself.
http://rumkin.com/tools/cipher/skip.php
Take K3:
ENDyaHrOHNLSRHEOCPTEOIBIDYSHNAIA
CHTNREYULDSLLSLLNOHSNOSMRWXMNE
TPRNGATIHNRARPESLNNELEBLPIIACAE
WMTWNDITEENRAHCTENEUDRETNHAEOE
TFOLSEDTIWENHAEIOYTEYQHEENCTAYCR
EIFTBRSPAMHNEWENATAMATEGYEERLB
TEEFOASFIOTUETUAEOTOARMAEERTNRTI
BSEDDNIAAHTTMSTEWPIEROAGRIEWFEB
AECTDDHILCEIHSITEGOEAOSDDRYDLORIT
RKLMLEHAGTDHARDPNEOHMGFMFEUHE
ECDMRIPFEIMEHNLSSTTRTVDOHW?
and count off every 192nd letter (starting on the 192nd letter)
SLOWLYDESPARATLYSLOWLYTHEREMAINS
OFPASSAGEDEBRISTHATENCUMBEREDT
HELOWERPArTOFTHEDOORWAYWASREMOV
EDWITHTREMBLINGHANDSIMADEATINY
BREACNINTHEUPPERLEFTHANDCORNERAN
DTHENWIDENINGTHEHOLEALITTLEIIN
SERTEDTHECANDLEANDPEEREDINTHEHOT
AIRESCAPINGFROMTHECHAMBERCaUSED
THEFLAMETOFLICKERBUTPRESENTLYDETA
ILSOFTHEROOMWITHINEMERGEDFROM
THEMISTXCANYOUSEEANyTHINGQ?
It’s interesting to note that the Q is not added but internal to K3 and the “?” is included in the transposition. I checked against the CIA’s page and Elonka’s and the Q is definitely part of the ciphertext.
So opinions aside, I’m not sure how anyone could argue that the “?” is part of K4 or that K3 ends anywhere but on that “?”. The crazy thing is that by this method, the plaintext ends at the only non-letter symbol which happens to be a ? which happens to end a question at the end of the section.
It seems to be a clear indication that K3 definitively ends there and that a new cipher awaits the analyst, especially as K4 only has 97 letters.
Kryptos - Beyond K4 
It seems weird that it could be this easy.
Since we have in K(2?) a pattern of using X for fullstop, perhaps the Q could represent ? and the ? could represent the punctuation for the K4 PT if it is reversed. Not necessarily that BERLIN is NILREB, though that would be possible I suppose, but that 69=B, 68=E, 67=R, 66=L, 65=I, 64=N, etc. Just sayin’
I’m going lately on the NYTimes article mentioning 97 and the NPR interviews where he mentions 97 as the letter count and that the ? is a ?.
You may not be off on thinking that K4 is not in the right order though. If you look at his notes for K1 (NY Times article), you can see two arrows. This suggests he contemplated some directionality at one point and may have kept it for K4.
Who the hell is Q outside of Bond movies?
A funny character in the Star Trek series. It took me 9 months to think of that joke
I have found several clues that led me to some sort of “proof” that
counting every 192nd character is the intended solution for K3.
1) One of the Morse codes texts reads: “T is your position”.
2) K2 gives us coordinates, that are located in the same courtyard as the
Kryptos sculpture: 38° 57′ 6.5″ North, 77° 8′ 44″ West.
3) Enter those coordinates into Google Earth and rotate the scene so that
the lodestone (and compass) point up (“North”), and zoom in, so that the
courtyard fills your entire screen.
4) On the top right you will find the “S” of the Kryptos sculpture, below it
is the small pool and the two stones — representing a “Q”.
5) In the center of the bottom of the courtyard is a large lying “J”.
6) If you now overlay the courtyard with the first (top left) copper screen
of Kryptos, which contains K1 and K2, you will find a “J” in the center
bottom position (in column 15/row 14), and an “S” and “Q” in column 27,
rows 7 and 8, at about the same positions as the sculpture and the pond
are.
7) If you now look at the position of the coordinates, you will find a “T”
in column 5 and Row 7 — the same row as the “S”.
8) That “T” is your position — and it is the 192nd character of Kryptos.