From watching your video's, I can guarantee the noise isn't comming from the sub bottoming out. //content.invisioncic.com/y282845/emoticons/wink.gif.608e3ea05f1a9f98611af0861652f8fb.gif I should have taken a video of the 12 I tested with 4 M1a's running it. My guess is that the box is making the sound from the woofer being loaded so hard against it.
Just my experiance with the AQ woofers, I would seriously recommend building your new box with 2 layers of 3/4 MDF. You'll gain a considerable amount of output and it will sound much better.
My 0.02 about the sub location on the baffle. I would center the woofer between the port wall and the side of the box, like DJ recommended. When you have the woofer that close to a wall inside the box, it causes uneven pressure on the cone. We went through many woofers in the Team Budweiser Luv due to that very issue. We had the woofers a little too close to the side wall of the box, and the coils would smack the top plate on the port side every time we poured some power to it. Thanks to DJ and Jassa's recommendations we were able to correct the problem. Funny thing is they helped us out, even though we were running MT's instead of DD's or AQ's. We called them trying to buy woofers because we were getting mad at the MT's, and they told us how to fix our crap so we didn't have to buy woofers.