For one, I remember that the asymmetrical frame-rail grommet likes to stay attached to the stock box upon removal, due to the hook-like mounting tab that hangs from the box. So make sure that you have it fully seated and in correct orientation into the frame before installing the INJEN box...
I had the exact same issue, as the inlet to the airbox was putting what seemed like undue pressure on the inlet snorkel, and keeping it from fully seating. I'm downloading some installation photos I took right now, and we'll see if I can give some more pointers. Give me a few minutes here...
It appears to be panel bond adhesive and/or sealant, but it might not be from the factory. I'll have to look at another one as an example.
Did you get your car used, and do you know if it was ever in an accident?
Pairing your BM3 with a catless downpipe and free-flowing exhaust, it'll likely pop little flames here and there on high RPM accelerator lift-off and full-throttle upshifts, with the tune it currently has.
I would absolutely advise you to acquire every nut and bolt on that list. Several of them are 'prevailing torque' style and can't be trusted to provide the same level of tension the second time around.
LOL the catless downpipe and spaghetti monstrosity known as the Boost Logic, combine their power to become the loudest exhaust I've heard in person on a MKV.