Simple solution. mix water and chlorine bleach 50 50, and use a brush to rinse down the shell, and or cover to eleiminate the mold. When the tub is filled and the pumps are started, you are going to get some ugly stuff coming out of the internal plumbing also.
If the water had been chlorinated prior to draining the spa, it would have eliminated, or at leaset minimized, the problem, but then if you do it "just before" draining, the chlorine can kill the grass.