Do you still have your original Agnus lying around? If so, remove the Megachip and replace it with the original Agnus. At least then you've eliminated any fault with the Megachip, the wire connecting Gary, the RAM, PAL etc..
I had a problem with my Megachip and my A2286 bridgeboard. The bridgeboard would intermittently freeze and then get a Green Screen of Death. It was the wire connecting to Gary that had broken within the plastic sheath and was losing connection as soon as the cable warmed up a touch.