My eureka was a bit premature. After more burn in time and more reads and writes it is still not right, e.g., it is creating bad directory entries - dupes etc. Good news that it seemed to work when cold but as it reached steady state temp it got flakey. It might even at this point be something as simple as a cold solder joint.
If re-soldering connections has no result I still think I am close but will now look at the signals a bit closer and walk though the code in comparison to the protocol charts in the IDE spec. I will look at software timing as well as hardware timing and signal characteristics.
More when I know it.
Rich Leary