More information next emerged that contained some clues to the launch trajectory. Now Cees Bassa has done an extensive analysis, modelling a trajectory. The details can be found here on the Seesat-L mailing list. He finds a launch location near 28 N, 68 W, more to the west than I initially thought.
I used Cees' results on the launch location and STK to fit a ballistic trajectory through Cees' launch location and the probable target area discussed earlier. The trajectory (visualized below) fits well with the altitudes and azimuths as photographically observed by Jan Hattenbach from La Palma (see astrometry in the appendix to my post here).
The trajectory STK fits allows to say something about altitudes and flight-times. The launch occurred near 21:10:40 UT. After a 36 minute flight over a distance of 8660 km, the target area between St. Helena and the Gabon/Congo coast was reached near 21:47:00 UT. In the top of its ballistic trajectory, the missile reached an altitude of
(note added 27 Sep 2013, 13:00 UT : Cees Bassa has since released the detailed data of his ballistic curve fitting: he has the apogee somewhat lower, at 1650 km, and a flight time between 21:10:00 UT and 21:44:45 UT, one minute faster. Please note that the diagrams below are based on the STK derived trajectory I cobbled together, not Cees' data.
Update 28 sep 13:00 UT: Cees' trajectory does not have the impact point in the published exclusion zone, but somewhat to the East of it. That is the major cause of the discrepancy between the results Cees published, and the ballistic trajectory I present here, which does land squarely in the exclusion zone. With the impact point shifted slightly westwards, the apogee altitude shifts upward if one wants to match the azimuth/elevation data from La Palma.)
The two events at 21:17:08 and 21:08:43 UT that I initially misidentified as the 2nd and 3rd stage ignitions, but which are, as Jonathan McDowell pointed out, likely the MIRV bus and MIRV separations, happened at 1130 and 1330 km altitude in the ascending phase, after 6.5 and 8 minutes of flight-time, 1860 respectively 2235 km from the launch location. They are marked in the diagram below:
(note: for this post I am much indebted to Cees Bassa and his fine analysis. His trajectory reconstruction provided the basis for the diagrams and the timing and altitude information in this post. Cees' own detailed trajectory data can be found here - they slightly differ from what I present above, but see the note elsewhere in the post above.)