I get the feeling it's evolving too quickly. Take a look at this analysis for some suggestions on how you might want to try varying your accompaniment to the ground:
Passacaglia & Fugue BWV 582
I agree that the ground can't always be heard, but that's the MIDI's fault. Putting the ground in the highest voice as echurchill suggested is a good idea, as is implying it without actually sounding the ground (as Bach does above). The only really awkward element of the ground itself is the tritone - that interval should really only be approached 'with daring', for want of a better expression.