Congrats on the new pipes!
I agree do not open up the airbox as it will only make popping worse..........
Same thing with removing the baffles, besides being irresponsible you will only flow more air leaning it out more and ......more popping
As you stated it sounds great right now so ............
I feel the same about my Arrow Ti with baffles, it sounds great, you can hear it coming and definitly hear it it going if on the gas but it is not so loud that it draws unwanted attention from

olice: or the :angel: .
Your best chance to have your system work with the stock tuning is to not do anything else except having your shop tweak what little they can to richen it up. I also think that pulling the O2 sensor will probably help based off of people that have done that and did a plug chop both ways. I will pull mine next time I'm in USoA and get to ride.
Every dyno I have seen that shows baffels in and baffels out of a full system there is VERY LITTLE difference in power. I think that you would realy need a built motor to be able to be able to capitalize on a full open system
go to bos-exhausts.com and look at their dynos on their systems.
Here is one, it shows stock, a full system with baffles and a full system without. It does exactly like I'd expect.
EIther of the full systems provides a good boost, the baffled system starts pulling a bit earlier, the baffle less system has a tad more on the top.
In the middle there is really no difference to speak of.................except noise........
http://www.bos-exhausts.com/cat/0300430r-eng.html