Hi Folks, here's a quick update with my story of my recovered Mac.
After what appeared to be an initial success I had an issue with the machine 'freezing' after a few minutes use. I've noticed that this seems to be a common issue for people with G5's so here's what I did to solve the problem.
I stripped the machine down completely (I'm an engineer so this wasn't really a big deal for me, but you do need a few tools like a long 2.5mm allen key, philips screwdriver, nothing serious. Always try and observe anti static precautions when you strip a system down, ideally do it on a dissipative mat with a wrist strap to ground.
So once I had the motherboard out of the box a problem was clearly apparent. There is a custom chip on the back of the board which may be some kind of memory controller or bridge. This has a heatsink and associated heatpipe assembly.
The heatsink is secured by 2 springloaded plastic lugs. These had both become unclipped and were not able to retain the heatsink in place. The custom chip was therefore clearly not being cooled correctly.
So I cleaned the old heatsink compound away and applied new, then replaced the plastic lugs with 2 off 3mm x 12mm nylon bolts, tightened it all up and reassembled the system.
The machine booted happily first time and has now run for several days without problems, I have restarted the machine several times and have not experienced any 3 flashes of the LED symptoms or any failures to boot up.
So I'm now pretty confident that this has fixed my machine, I can't guarantee it will solve all of these but its definitely worth a look.
In fact, the problem can probably be diagnosed without disassembly. If you look at the main board between the sets of rams, and towards the processors you will see a cluster of components, these are the decoupling passives for the custom chip. The ends of the 2 plastic lugs should be poking through the board 3 or 4 mm at two corners of the cluster. If the lugs aren't sticking through then the heatsink will be loose and the custom chip won't be cooling properly.
Hope this is useful info for someone.