At DANCE we have a similar issue.  We are still doing "software
handshaking" between multiple frontends (15 which read data, and 16th
with direct accessto the trigger logic), and we apply a time stamp
using gettimeofday().  We use the regular mevb, sorting on serial number.

In the analyzer (MIDAS or ROME) we then keep a big circular buffer of
event fragments, which are rebuilt into new events based on the time stamp
obtained from gettimeofday().  We keep the system clocks synchronized
(often to within about 1ms) using ntp (need to average over several
ntp servers to avoid issues with network noise).  ntp can take a while
to stabilize, so we never reboot our computers... (well almost never).
We have a slow control frontend which monitors the ntp time offsets and
put's them in the history system for easy visualization.

Occasionally we seem to get in a mess, but somehow this fixes itself on
the next run, so it has been a useable system.  Maybe one day we will
get hardware handshaking between the frontend computers and the trigger
logic, but in the meantime we are taking data.

John.