Be very careful interfering with air intake! Why are you so adament that you don't want to replace the box, it makes no sense to me?
My advice - simply find another replacement box.
Some air filters require re-jetting and quite honestly this is too much fuss for me. I have left the OEM box in place and put a Pipercross foam air filter in. The engine seems less strangled and probably produces a few more hp.
Surely it's worth looking for a secondhand replacement.
How are you intending to use the bike - offroad or onroad? the answer will dictate what you will need to do.
I wish you well whatever you decide.
Triumph Bonneville 800 (2004), Yamaha XT600E (1999), Honda XBR500 (1986).