Lay the Gasket on a white paper towel over night. See what colors it turns.
I'm wondering if most of the staining is oil, and you happen to have a small coolant weep near the coolant passages.
I'd still seal the bolt threads when you reassemble. Like AJ said, they should be blind, but aluminum castings have a way of seeping through porosity sometimes. It hurts nothing to seal the threads.
If also put a small perimeter application of right stuff around the coolant passages.
