Maybe you could use something like a serial to parallel
converter chip or the serial port input of a microcontroller. You could
feed in a constant string of zeros until an event, and then feed in a one
to the stream when the event occurs. You could save the stream of ones and
zeros in memory for maybe a second, and then stamp the block with the
time. Then you can have your main CPU figure out the time of each event by
knowing the bitrate and looking at how many bits precede each one bit back
to the beginning of the block. The blocks would likely be largely zeros,
and would thus compress really well if you decide to not even bother
converting the format of the blocks to a timestamp format. The advantage
of this scheme is that it could probably have a sampling rate far higher
than a timestamping process, without overstressing even many modestly
powered processors.
Another way to synchronize your samples with GPS, at the cost of some
sample rate, is to use a two input multiplexer at your serial input and to
take every odd bit of your serial stream to be a sample of the pps output
of your GPS and every even bit to be the state of your event trigger. That
way your pps and data are interleaved in your bitstream for post
processing.
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