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I assume you are using premium gas. If not you should. Check the plugs. If they are white the bike is running lean.. Make sure the gap is set correctley for your bikes spark plugs. Also check the jet sizes in the carbureator for your modifications and elevation. If the bike was fine and just needed a tune up i would pull the map off and reinstall the stock one.
Changing to a K&N air filter changes the air/fuel mixture for your bike, and you're probably hitting an overly lean spot before things start to even out. For bikes still running carburetors, which I think you have, you can compensate for this by changing to a slightly larger idle jet. Your main jet is probably fine (it's kicking in after the lag); it's the crossover from idle to main jet that's causing the flat spot.
Talk to your dealership parts counter to get recommendations about jet settings. They may suggest, for example, to keep your existing idle jet and go with a different main jet. Expect to try a couple different setups to find one that works best for your bike and your riding style. I would highly recommend keeping your original jets, though, in case you ever go back to the stock air box.
I expect the lack of back pressure from the new exhaust pipe will have a lot to do with it. If there is not enough back pressure, the reed valves won't work properly and no fuel will enter the engine. Try the old exhaust system to find out.
When the carburetors over flow enough to fill the exhaust, It is possible that the gas also went into the cylinder and flowed past the rings and into the crankcase. With the engine overly full of gas and oil you could easily pop a seal or blow out a gasket. Check your oil level. If it is too full , change the oil, it will not lubricate properly with all the gas in it. Check that your shaft seal has not popped out. Check the air filter, the breather may have blown oil and gas all over it when you started the bike. Empty your pollution tubes behind the motor( they will drain the air box). Get in the habit of turning your fuel petcock off when not riding. This gas flooding happens randomly in certain models but can happen to any one.
the batery is ok if the engine start avery time. Also the volts are ok. Have you made any modifications on it? Sport exhaust, sport air filter? Check also the air filter. Make sure is clean... Idle speed should be around 1000-1200 rpm. You should have a screw to fix the idle speed. Check it on the carburetors area, or download the manual from internet.
you put too much oil on your engine, 2.8L without filter change. 2.9L with filter change is the recomemded if you exceed you bike will spit the excess oil sometimes the oil goes to air cleaner have your air cleaner check and cleaned
Sounds like it's running lean. Almost everything you mentioned here would cause a carb equipped bike to run lean and cough and sputter and stall. Since you bike is fuel injected, I cannot help you. If it were mine, I'd take it to someplace that could put it on a dynometer with an exhaust gas analyzer. They may recommend the installation of a PowerCommander. Your local dealer may can change the fuel map.
Yes , You can By-pass the afterburner , but! have the engine tuned following doing that as it will not be running the correct air/fuel ratio. I fitted a Power Commander PC111 USB with a zero map , and had the dudes at Dyno Jet run it up on the Dyno and create a bike specific fueling map for it. It is AWESOME !!! I run 98 octain fuel and the air fuel ratio is 13.2:1(K&N AIR FILTER ALSO)