You should have double checked that box.
For now instead of ordering a new box just take that bish apart and use the wood to throw together a diff ported box or even a Sealed box. That would be one way to see if the sub still makes the sound at high volume.
Also, check those VC's and make sure each one still reads 1.5. Another thing, do you have that sub wired in series at 3ohm? Because if you have it in parallel it could be at .75 and you could have the gain high enough to clip that thing.No man that was your sub most likely bottoming out. DO NOT run it anymore in that box. I had a good feeling that box was too big. You measured wrong or something when you built it. If you want, im sure you can still build it to that size with the box you have, you just need to take it apart and trim it and put it back together. Id trim the parts with the glue as much as you can to make it easier to put the box back together. The sub is more than likely still good if its not making noise all the time, its good. Dont worry about it. DO NOT buy a box on ebay.. Resize your current box and you will be happier.
Just use the dimensions from that plan you linked. That will make it alot easier. And remember, measure twice, cut once.
EDIT: By the way, it may not be quite 4 cubes if you didnt subract the port area. But either way, the box is too big and that was the problem. I strongly suggest just resizing the box to the plan you linked.The list goes on... maybe you can show a little gratitude/humility, and read the advice that people spent time posting...It's possible you're hearing the sub unloading at high volume from being in such an oversize enclosure.
You're not screwed. You need to find out what the port displacement is and subtract that from 4.2 to find the net volume. JL recommends 2.375cf @ 34.59hz. You can glue some 2x4 blocks inside or wall off a portion of the box to reduce the volume, try to get down to around 2.5cf. Double check the tuning, it'll change when you reduce the volume.
The other option is to start over and use the rec'd box dimensions on JL's website.