The 466MHz CPU board probably came out of a DA, so the speed in a Cube makes sense: 466 in a DA is 133 x 3.5, so the Cube with a 100MHz bus runs it at 350MHz.
Is temperature a factor? Is it more stable when cold? If you run it out of the case with the boards exposed, can you press on chips, flex the boards, slightly bend wires/connectors, etc. to locate the problem? Are the boards dirty/corroded? Contact cleaner on the various connectors may help. The 300-pin connector for the CPU is a bit fragile and its pins are easily bent or contaminated.
Also, I've worked on a few Cubes that had a factory bodge applied to a regulator, which runs very hot. Does your board have this bodge, and do the components look intact?