Choose clock buffers carefully. Likewise, noise on clock lines is Very Bad. We recommend series terminators on the clock lines, because they are simple, and each line can be tuned to the circuit board, which can improve signal quality and reduce skew. It is, in general, futile to attempt to troubleshoot a PowerPC system without access to the buses. So the best thing to do when confronted with a fail, is to instrument the buses so that you can see exactly what is going on.
Scopes are nice .
Sometimes the failure is digital, and sometimes it is analog. Remember that the logic analyzer may actually be interpreting the signal differently than the device. So a good scope should be used to verify that the signal levels and timing are appropriate. Check the signal quality before and at the time of the fail. This often means examining each suspect signal with the scope.