Whenever a system becomes inconsistent, I try to use a clean install on a separate hard drive. If it's still problematic, I swap ALL the memory. If problems continue, I tear down the system, dust everything, take the heat sinks off, clean everything with alcohol, put new compound on, and reassemble. I check that all of the fans run while the system is on.
Many, many G4s with the paper-like stuff between the processor and the heat sink become flaky because the CPU card warps a little bit over time. The G5s aren't immune to the problem, though the compound they start with is usually better.
If you don't want to risk permanent damage, don't wait to replace the compound on the processors.