OK, I'm going to take a stab at A & B. First, I've taken some time and refreshed myself with the pertinent rules. The first problem is that the example given on page 92 about the Skimmer waiting, is an illegal maneuver unless this was amended by Thom somewhere on the forums.
When taking a wait action, the model must end it's turn. The wait is the last thing that the model can do. Now with Ambush, the model is allowed to take a second wait action but, the normal rules for going on wait still apply. So, the gunner would not be able to wait, wait, then act. A Free Marine would not be able to wait, wait and then shoot. This is never a problem though because it is a single model so it would just shoot first and then wait.
So, the first question is do we ignore this inconsistency and assume that the Skimmer was designed to be able to pull off the maneuver that was given as an example. I would say yes because it is blatantly given as the example.
So, this brings us back to the original question. So now we need to consider the dynamic nature versus static representation of the game. If the Skimmer is moving than the gunner would not get his +3 bonus. So, we need to figure out what designates that the Skimmer is moving. Reasonably I would surmise that if the driver moves the Skimmer with all three of his actions then the Skimmer would be in motion for the entire duration. So, if the gunner waits then he would not get the +3 bonus. So far pretty straight forward. So, based off of this assesment, I would go further and say that if the driver moves the Skimmer on his third action while the gunner is on wait, then the gunner is attempting to fire while the Skimmer is moving so no bonus.
In summary, at this moment if I was moderating a tourney, I would say A)he gets the bonus and B) no bonus.
I hope that this makes sense and is helpful.