get temp monitor
http://www.bresink.de/osx/TemperatureMonitor.html
and log the temps of the CPU's and see if you get a thermal runaway.
the max is 68 C degrees for my Dual G5 but it may be higher (like 80 C)
for your liquid cooled G5.
Also just before a runaway it should be logged so open Console and look at your logs
If you are getting thermal runaways then first do the basic stuff like open case
and blow out all dust and check to see that All fans are working and heat
is coming out BOTH vent grilles in the back. If only one grille is hot then you
may have a bad fan, or heat sink not installed properly (may have come lose) or
your G5 needs a temp re-calibration. In that case use the G5 diagnostics DVD and
re calibrate.
You can always add more fans
if still problems then you have a bad thermal diode on one (I doubt both) CPU's or a BAD CPU
in which case you will have to take it in for repairs.
good luck