So then the TOR tune did nothing. Removing the plates and installing freeflow exhaust has most likely leaned the bike some, freeing up the intake air will most definitely lean it further.
Cutting holes in the air cleaner box would make little difference since it's the narrowest point and the bends in the rest of the system that make for low pressure.
If it's a lean condition he's concerned about, it's doubtful he's made enough change to cause a problem. If it's performance he's after, well ... there are better methods to the madness. A K&N undertank filter for instance ... that would eliminate one of the worst and most restricting bends in the system while still keeping the intake quiet. Adding something like that to a bike with TOR's will for sure require a remapping of the fuel to avoid it being too lean, but would also insure an easier/better breathing motor.
Pig's photo shows what I'm referring too, it's easy, quiet, cheap and breathes very well.
That filter box under the seat is such a valuable storage space on a bike that has no internal space at all factory, that I cringe just thinking about cutting holes in it.