Assuming the three-bass scenario led me to originally conclude that Carl must be playing the guitar, but as I later pointed out on this board, and as you mentioned above, the jazzy guitar doodling between takes points to a studio pro rather than Carl, and according to someone on this board, Terry Melcher had gone on record as saying Carl did not play on the session. If Bruce was recalling that he did, perhaps he was thinking of a different session (do we have a source for that Bruce quote)?
In the September 1990 edition of Select magazine, Bruce makes the following observation about the GOK session:
"I was there!...Carl was in the booth playing 12-string cos there was no more room. And there were about six fiddles - we didn't call them strings, they were fiddles - and an electric bass and an acoustic bass and a keyboard and some percussion, and the guy who's playing the drums."
Hmm...well, maybe Carl and Carol BOTH played 12-string on this session (the way Carl and Jerry Cole both played 12-string on "California Girls", and Barney and Glen both played 12-string on some of the other Pet Sounds cuts). Carol definitely played 12-string electric on the second session of "Good Vibrations" (April 9th at Gold Star), and most likely on "I'm Waiting For The Day" (similar situation to "GOK" - apparently only two basses, definitely Ray on the Fender and Lyle on the upright, leaving Carol as the probable guitarist) and the basic track to "Caroline, No" (although she also overdubbed the Dano bass on that one).
Also I thought I would bring these up. I have no idea if these are reliable sources or not. I am dedicated to get to the bottom of this!
http://www.surfermoon.com/essays/owncharts.html Carol
http://abbeyrd.best.vwh.net/carolkay.htm Carol
https://www.youtube.com/watch?v=XByMda7YooI Isolated strings, horns, percussion, and bass
https://www.youtube.com/watch?v=QCTVcNsJGX0
Again, I don't know if these are reliable