When it gets sorted out, it will a snap to work on it. Based on you said you hear the pump running but nothing is happening, it sounds like there is an obstruction in the pump or line, or the valve is not actuating. The system uses a self priming pump, so that shouldn't be an issue. The biggest thing to pay attention to is the 3 probes in the ballast area. If they are black, then the pump controller will not work properly. The upper probe stops the pump when the tank is full, and the bottom 2 allow the pump to operate to pump out water, if they are not conducting then the pump will not empty the tank. They are pretty easy to clean. There are a lot of people on here operating one of Bob's systems, I am sure any one of us can assist you if you need it. The stuck rudder can be as easy as a broken linkage or it could be a bad servo, although i have only seen a bad servo 2 times over all, that doesn't mean i can't happen.
When surfaced, the bridge access hatch can be optionally open or shut, however, when submerged it is required to be shut. (Really a no s***t precaution from a procedure in use in the sub fleet today.)