If it's popping through the exhaust, wouldn't that mean a hydrocarbon backfire? The bike may be too lean, now that it's running less restricted, and needs more fuel. This would be a Main jet, and pilot screw adjustment. You have to do a Spark Plug reading and see how they look to determine if the bikeis too lean or too fat on it's mixture. I don't see the pilot jets affecting this much really, except at idle. Maybe someone else can chime in.?
Pilot screw adjustment
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Has it been doing this for 2 years? Usually when a bike is running too lean, unburn fuel, unable to combusts, does so in the exhaust chamber. It's called a "Hydrocarbon Backfire" and does not happen under acceleration, it happens on deceleration. Vehicles these days tend to be run lean, so you hear little pops, but on motorcycles with headers just put on, by letting more air flow, you are actually making the motorcycle run in a lean condition as there is too much air not enough gas, resulting in poor combustion and the combustion happening in the exhaust when you let the throttle down, as the heat and unburnt fuel now combusts in the exhaust pipe. You need to do a plug reading first, to eetermine if the mixture off the Mains are running lean, right on the money, or too fat. If it is running with a nice Tan color, then you could try playing with the pilot jet screw, this is easy enough to do, and if it eliminates your problem, you are all set. Did the manufacturer state "No Jetting Necessary" with the exhaust system. Most bikes have to be jetted when you go to a header. Even when the after market pipe states "no jetting necessary". Try the pilot jet adjustment. Take a spark plug out and see what it looks like. It's not hard to do and will let you know much. Too lean of a condition will burn your exhaust valves out, too fat, the spark plugs will blacken. You don't want to run lean, it will do more damage than good. Since the pilot adjust procedure is something you know how to do, why not? If it clears it up, still take a spark plug reading so you know that you're getting all the ponies you bike shold be giving you. 
Thanks again for taking the time to reply,Has it been doing this for 2 years? Usually when a bike is running too lean, unburn fuel, unable to combusts, does so in the exhaust chamber. It's called a "Hydrocarbon Backfire" and does not happen under acceleration, it happens on deceleration. Vehicles these days tend to be run lean, so you hear little pops, but on motorcycles with headers just put on, by letting more air flow, you are actually making the motorcycle run in a lean condition as there is too much air not enough gas, resulting in poor combustion and the combustion happening in the exhaust when you let the throttle down, as the heat and unburnt fuel now combusts in the exhaust pipe. You need to do a plug reading first, to eetermine if the mixture off the Mains are running lean, right on the money, or too fat. If it is running with a nice Tan color, then you could try playing with the pilot jet screw, this is easy enough to do, and if it eliminates your problem, you are all set. Did the manufacturer state "No Jetting Necessary" with the exhaust system. Most bikes have to be jetted when you go to a header. Even when the after market pipe states "no jetting necessary". Try the pilot jet adjustment. Take a spark plug out and see what it looks like. It's not hard to do and will let you know much. Too lean of a condition will burn your exhaust valves out, too fat, the spark plugs will blacken. You don't want to run lean, it will do more damage than good. Since the pilot adjust procedure is something you know how to do, why not? If it clears it up, still take a spark plug reading so you know that you're getting all the ponies you bike shold be giving you.
I will do a plug check to see what colour the plugs are. The manufacturer stated no jetting required and I can confirm the bike runs perfectly, no flat spots or misfiring at any time other than when throttle is fully closed. Yes it has done this since I fitted the exhaust. For me to richen the mixture on the pilot circuit do I turn the screw in? I was thinking quarter of a turn as a starting point.
Andrew
I agree with using the 4 into two exhausts. I found raising the needle one notch on my bike reallly made the mid range power increase, and took away the need to feel I needed to rev the engine for power. I could let the engine work, and feel it pull without revving, but pulling with more torque.
Thank you. Thats what I thoughtFrom what I have read, screwing them out leans the bike out, screwing them in fattens them up. That's what I've gleaned off the web. It would be well worth getting a Factory Service Manual. It will return the investment in in $1000's of dollars of savings of aggravation.
If you look at all the GT3 racing, and similar cars), all the cars let off that popping sound when off the throttle. It's just part of the "Mean is Lean" phenomena. Manufacturers put of these 25 lb. mufflers to get rid of that sound. The new exhaust cans I made for my ZR1200 knocked 42 lbs. of the weight of the bike. Running too lean is a problem, using only the amount of fuel you need is the goal. The popping sound will become familiar, and itself will tell you if another problem arises if the sound changes.
Thanks for taking the time to reply, I have checked the plugs and they look correct, so I am not worried about it.If you look at all the GT3 racing, and similar cars), all the cars let off that popping sound when off the throttle. It's just part of the "Mean is Lean" phenomena. Manufacturers put of these 25 lb. mufflers to get rid of that sound. The new exhaust cans I made for my ZR1200 knocked 42 lbs. of the weight of the bike. Running too lean is a problem, using only the amount of fuel you need is the goal. The popping sound will become familiar, and itself will tell you if another problem arises if the sound changes.
KISS (KEEP IT SIMPLE STUPID) is an addage we always followed when flying, when machining, building computers, fixing circuit boards, etc.. A lot of presumptions in the previous post. As you have done a spark plug read, and you have found it to be the right color, there's no point of talking about adjustments to a carburetor that cannot adjust that way. You could just for a set of "Flat Slide" carbs, and nasty header, start the whole process with the bike ending up on a dyno .
Great video though.
Great video though.
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