I have read that 500rpm is where "it's at" with suggestions that faster doesn't adequately crush the grain. A second run sgould remedy this but, might also pulverize those that were milled adequately on the first run, if they pass between the rollers just right.
I too have issues with my drill set-up. However, my issues are mostly due to being too lazy and hand limited to hold the drill. Perhaps the "engineer" in you might be able to devise a way to disect and re-mount your drill and it's variable speed switch to find the best rpm and keep it hands free.