I would be talking directly to Apple Customer Relations at this point.
Meanwhile keep logs on those kernel panics.
My guess is that something is loose from when they rebuilt your machine.
This is really a shame. Most of the major G5 issues I've followed relate
to the original 2.5 GHz towers and the 2.7 GHz liquid cooled models.
The orginal 2005 "Rev B" 8DIMM PCI-X 2.0GHz and 2005 2.3 GHz models
have been much more reliable.
A few did have power supply issues causing the chirp, but that was fairly
easy to resolve with CHUD Tools.
Hopefully Apple will upgrade you to a Quad and that will be the end of your
troubles.
Generally when a machine undergoes this many repairs without solving the
problem Apple will probably " recover " it.
I'm thinking you should also run your system through a good power
conditioner if you aren't already doing so.
When I install the electric meters on most residential services, the voltage
can vary quite a bit, from 2-7 volts higher in many cases.
This can cause major problems for sensitive electronic equipment.
It wouldn't hurt to have your local power company come out and inspect
your meter base to make sure everything is ok in there.
Just tell them, you've been getting some voltage irregularities and want to
be sure there's nothing going on in your meter base.
It won't cost you anything and frankly many meter bases haven't been
opened for decades, so it's worth it for peace of mind.
I can't count how many services I've opened up to find loose connections
and completely cooked service entrance cables and meter blocks.
Considering the amount of money you've spent on your system, I wouldn't
think twice about a power conditioner and a whole house surge protection
set-up.
This may not be the cause of your current problems, but it may prevent
future headaches.