Ok. It's a K&N or K&N copy. I would suggest a foam UNI filter, since they filter a lot better, but I'm assuming you're going for looks. Yes, you will likely have to go up one size on both the main and pilot jets, and turn the pilot air screw out a bit more. Without an emissions analyzer, the only real way to check it is by the way it runs and by the color of the spark plug insulators. Put 2 new plugs in it, and run it with stock jetting first. put 100-200 or so miles on it, city and highway riding. Pull the plugs and check them. If they are a dark tan, you are ok. If they are a light tan, you are too lean, but not in the danger zone. If they are white, you definitely need to richen up the jetting ASAP. Go up one size at the time until you get a dark tan color, putting new plugs in it every time. Don't throw away any of the plugs, they are all still good, and can be used as long as any new plug, once you get the jetting right.
I would advise not trying to run straight pipes with that filter. That would create more air flow that the carburetor can be tuned for. You can put home made baffles in straight pipes that will help create back pressure, bu8t if you decide to use aftermarket mufflers, I suggest the Emgo shorty ones like BCB sells.