frodo,
If you really need the second 100 amp panel due to load requirements, you might end up shutting down the first 100 amp panel due to overload.
It sounds like a co-ordination issue. Can you feed the second 100 amp panel from the main panel.
Also, do you mean 4 #3s?
And, as has been seen before, using the EMT as EGC is hotly debatable.