That was a post mainly for anyone else seeing your thread who might be interested in building their own box and confused as to why there's all these suggestions for simply sealing up the interior. A few others hit the nail on the head (no pun intended) and I just wanted to back their posts up.
I’m not telling you to redo it, but a couple of your posts in combination with the suggestion of bondo to fill the holes made me think these gaps are larger than just small holes.
Yea, building it is the best part. Sure. But, if you’re in a rush, or you simply don’t have the means, there’s no shame in having them cut it for you. I built 4 separate enclosures for one driver once… I had HD cut them all. Probably saved me a day when it only cost me about 30 minutes of waiting and a few bucks tip to the dude who cut it for me to show him my appreciation (and so I didn't have to pay the $.25/cut fee to the store).
Enjoy your box. Use silicone… call it a day. If you need more than what silicone can do you need a new box.
Sounds like you’re good to go, though. Rock n Roll! Let us know how it sounds.