Just a small update: I've heard another report of similar issues with Alice's Vbb voltage collapsing, but there the root cause was the C2X capacitor going bad (low capacitance), so that should also be considered if the same symptoms arise: graphics and sound goes crazy after a short time running OK, Alice runs hot, XU9 GAL runs hot, Vbb voltage and CCKQ clock voltage collapse, but cooling Alice avoids the failure.
My fixed A1200 is still going strong, so supplying Vbb externally seems an acceptable solution (provided C2X is OK). 
Do we know if this is also the same issue on the A4000?
Great diagnosis work. It’s always been documented that Alice can get hot. I always placed Heatsinks on mine and the GALs.