Little late to this thread but I've just been catching up... I listen to Danica's radio every race that I'm able to.
About midway through the race she reported that she had lost 1&2 gear as they were getting ready to pit under a yellow flag. The funny thing was Gibson told her to watch her speed when pitting and she told him to have Johnny K (engineer) give her a new tach reading for pit road speed in 3rd gear (which he did). Then a little later she told Gibson 3rd gear was now gone. Before the pit stop incident with the 15 she definitely only had 4th gear (she didn't suddenly lose the transmission during that pitstop...it was an ongoing issue in 2nd half of the race). During the late cautions they were letting the cars behind her know she only had 4th gear so they wouldn't get run into from the rear. During the late cautions she was reporting the transmission was sounding really bad and when the final yellow fell they were planning on dropping to the back of the field for the final re-start because of the transmission issues.
Just thought I'd confirm what I heard on the radio as the race was unfolding... This isn't something they made up to explain a pit road incident.