Box too big shouldn't be a problem. Boxes that are too big may reduce the amount of power required to reach full excursion, and may affect the response curve of the woofer. But I'd doubt that it would reduce the output.
Ports too long shouldn't be the problem. The longer the port, the lower the tuning frequency. If the port was too short and tuned excessively high, you might have a problem with wave cancellation. But your definately not too long... (I bet you've heard that before).
When you say that the box is flexing, this leads me to believe that your subs are moving pretty good. Is this true? Because, if your subs are moving, then they are displacing air, which leads to loud bass. If this is the case, then your mounting location for you subs is probably the problem. What kind of vehicle are you using, and how are the subs positioned in there? I have an Accord and I had the subs directly against the back seat. It seemed really quiet. I turned the box around and the volume was much closer to what I expected.