I have read this repeatedly, and I am afraid I need more information, because I don't understand it.
You seem to be saying two very different things here, but as if they are in fact one thing. You say your left foot weakness inhibited thrust and underwater maneuverability. It might do that, but there is no requirement for that. Then you talk about that being the reason you are not passing the navigation standard, which is indeed a requirement. That requirement will require you to swim in something like a straight line, but not at any particular speed.
Are you actually saying that you are having trouble following a compass heading, and the instructor is telling you that your left foot weakness is making that more difficult for you? If so, then that is a problem that can be overcome with a little practice. It actually happens with some frequency. I have seen students who are not using the compass correctly swim a tight circle instead of a straight line because of their uneven kicking.