If you synchronize and clean the carburetors the bike will not have the same power that it did before you removed the baffles from the exhaust system.
The baffles created back pressure in your exhaust system that restricted the flow of the exhaust gasses. When you removed the baffles it allowed the engine to 'breath' easier due to the lack of restriction.
Restriction in exhaust systems are designed for several things.
to restrict gasses flowing into and out of the engine. This means that you can use less fuel to operate the vehicle and allows the manufacturer to advertise a better fuel economy for the vehicle.
Better for the environment. In order to meet EPA regulations and such. Restricted exhausts allow for less exhaust gasses and....better for the environment.
Better bottom end power. At the lower end of your RPM range you will have more power which makes the vehicle more user friendly driving in the city.
The free flowing exhaust allows more gasses to pass through the engine and thereby requires more fuel to enter the engine to be burned. The condition you are experiencing is a lean condition.
You can drill out the air screws at the tops of your carburator CV cover closest to the head. They are aluminum. Be careful, your drill bit will go right through them and the aluminum plug over the air screws might just come off in the bit. That's ok, just don't penetrate to deep, you will hit a brass air screw if you do and drive it into your carburetor breaking off the the pin at the end of it. Once you have access after removing the aluminum plug blow out the aluminum shavings. Turn the air screw down all the way and turn it out 1.5 times as a starting point. Turning it out makes the pilot/idle circuit operate leaner, more air for more turns out.
This may resolve your issue but probably not. It will make your lower RPM's richer.
For higher RPM you will need to order the next size up main jet and a jet needle that has notches at the top. The jet needle goes into your throttle. The jet needle rests at the bottom of your CV piston valve.
You will raise and lower the needle by changing the clip position on the jet needle. If you want to make it richer, drop the clip to a lower notch. If you want to make the engine run leaner, raise the clip to another slot to drop the needle down lower into the main jet stand.
This procedure will allow you to tune the carburetor.
K&N makes a jetting kit for your bike. Jet kits are typically applied to carbs after a free flowing aftermarket pipe is installed to richen the system. In your case, it's just a modified stock turned into a free flowing system. It should work just fine.
Cheers
CV Carburetor Image
Notched Jet Needle Image
