You really should put the stock box back on, and you can bend the bracket out to help it clear the seat if you need to. The airbox boot is also angled, so you can rotate it to allow you to bend the bracket out farther to clear the seat, and don’t be afraid to trim a little material out of the lip of the seat, but that is the last thing to do.
The filter is pushing more air into an over carbureted engine than it can handle. We played with one for a while with no success. You would need to richen pilots, needle, floats and main to start, and It would probably need a different atomizer to run well.