Yes, the GSS6400 (GSS6425) can synchronously record the 1PPS event from a receiver as well as capturing the RF event. In fact it is possible to capture 2 synchronous data streams at once.
The data is stored in the same file as the raw GNSS signal. During play back the data will be played back at the same time as the GNSS signal file. It is not possible to view or extract the data that has been stored apart from at playback.
The data is input and output on the bi-directional IF connector; pin6 for channel 1 and pin7 for channel 2 (if you are only recording one channel the signal must be present on channel 1 i.e. pin6).
The maximum sampling rate is dependent on the type of file being recorded. 500kHz is the maximum for GPS/GLONASS recordings (*.dgg, *.dga and *.dgl types) and 250KHz maximum for GPS only (*.dat or *.dgp types). Exceeding these rates is not recommend and will result in a large number of errors on playback.