I assume when you built the box up (using the stays, etc from the old box) that the inner airbox plate sits correctly in the recess in the airbox upper half?
I put one of these box's on #302 a couple of year back, and must admit to having had to remove the sealing rubber from both sides of the air filter to get the airbox to close up fully. At the time I put it down to the fact I had used a pattern air filter that was just bigger than the original Honda one. Must look more closely when I get to put the re-painted box back on it.
Cheers - Chris R