http://mobile.jlaudio.com/products_subs_enclusure.php?series_id=10A Slash series 1000/1 and 13w7 is a good combo, but very particular. Take out your owner's manual, and it will show you exactly how set the amp for that sub. Sounds like the input sensitivity is too high to me. Should also have infrasonic at 25Hz, and JL recommends a 30Hz tune for that sub. Tune shouldn't be a big deal, but input sensitivity makes all kinds of a difference on those amps. It's not a volume knob.
I like this part...
Built to JL Audio's EXACT specs for a 13W7 woofer
Double-Faced Front Baffle (for added woofer support)
Net Int. Volume: 2.375 cu. ft.
Tuned @ 34.59Hz for MAXIMUM "SQL"!
Gold-Plated Speaker Terminals
Show-Quality Custom Carpet
Dimensions (W x H x D): 25.25" x 17.25" x 16.5"
JL specs are for 30Hz.
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.
Shit dude that sucks. You should have double checked that box.
So is that the box that the 10 was in?!
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.