I've never really looked at the separator in the airbox, my 03 TA didn't have the 2 rubber bits in there so I just pulled the main snorkel...
But.. if you drilled a clean 70mm hole in there, try putting a plastic plug or a button plug in that hole and see if the problem goes away. That's about the only mod you have done that varies from what a lot of us have done. There may be turbulence affecting the fuel/air mix.
Synching your carbs might help also, if you haven't done that yet.
