Start by disconnecting external components and find if the problems continue to exist when those are disconnected. If the problems go away with external components disconnected, then reconnect individual connections and/or pairs of connections until you find the source.

The problems might also be internal physical electrical problems, which could be due to loose or oxidized connections, more especially to grounds, or may be due to a leaking electrolytic capacitor. Try removing and reseating the PCI expansion boards, the connections to the daughter boards, and connections to the power supply. Take the time to look closely for any leaked electrolyte on circuit board surfaces and look for swollen and/or leaking electrolytic capacitors, and remove any accumulated dust.

If/when you find the problem, please report back with follow-up comments.