There's still air in there somewhere. If you've done the handbrake cycle, then the rears should be clear now. You can flush the fluid in the ABS by engaging it a few times. That changes the fluid, but it won't clear air - only a dealer can do that. Now, you've described the situation as never letting the reservoir get too low, so that shouldn't be a problem, but if you've got stainless lines, then there's no reason you should have a mushy pedal. It will go a long way down if you really stand on it, but not all the way to the floor.