Don't know if this has been written up before, but here's my version.
This will help you if you're changing out the whole exhaust system as far as removal of the header pipes go. Once you get your ECU flashed (I had mine done at AF1) the flapper is not in use anymore, which is fine by me. So, I decided to get rid of the flapper itself, and the actuator motor. With the ECU flash, you get no warning light when you remove the motor. I wanted the flapper out of the exhaust. I didn't want to find out that it got stuck in the closed position after removing the motor and cables. So, let the fun start. It's all easier than it looks, but you need some patience to figure out little things like how to remove the bodywork side panels. Reason for that is you have to remove the front two headers to pull them forward to get the rear collector off. (Make sure you order two new exhaust gaskets #852090) This sounds like a lot of work, but I think I had it all off in an hour and a half. Ok, back to the side panels. There are two push/pull tabs on the inside of the panel at the top. You just need to remove the rearward one. And the one on the lower area on the inside. They come out rather easily once you get a thin screwdriver in the groove to pop it open, and then it just pulls out. Then take the two stainless allen's off the front top of the radiator to remove the black cowl that goes around the top of the rad. My bike has aftermarket signal lights on there, so not wanting to unplug it all, I just duck taped them up out of the way. Then go to the bottom of the radiator and on the right lower side, there's a cir-clip that you just put a screwdriver blade in and twist it till the clip comes off. Then push the pin out that the cir-clip was attached to. You do this because the oil cooler stays in place, but the bottom of the rad is pushed forward so you can get to the header bolts. You then go to the left side of the rad, and remove the bottom hose to drain the rad fluid. Just pinch the clamp and it'll come off. I strongly suggest a pan under it. You'll need a hose clamp because the factory clamps aren't reusable. Once the hose is off, push the bottom of the rad forward. I use duck tape wrapped around the bottom mount, and then push it forward and tape it to something like the fork tube to hold it there. Do not hit the fins with anything! When working on the manifold nuts watch your clearance distance from the fins with your wrench or hands, anything! They bend if you breathe on the wrong! Now take the four header bolts off. 10mm. Then move to the rear and remove the endcan. It's held on by a strap bolt, clamp, and a rubber mount on the inside that you may not see until you've pulled on it ten times. Trust me on that one. Then remove the two locking nuts from the actuator cables and the 13mm nut holding the flapper mechanism in place and pull the crap off the collector. Then go forward and remove the motor. Two 8mm bolts hold that on. Unplug it from the harness, and tape up and zip tie the harness out of the way. I put two smaller bolts in to fill the exposed holes. That done, move to the other side and remove the springs that hold the exhaust sections together. There are three of them. You'll need a spring T wrench, or slide some wire (like coat hanger wire) over the hook and pull on it with locking pliers. Once you have them removed, you can now pull the front section forward, (the front headers have to come out of the exhaust flanges. That's why you need the exhaust gaskets) and the collector down to remove from the rear header, and reward to set the collector free. Now you have a clear shot at the insides of flapper-valve. There are two screws holding the actual flapper in place. They are welded. You'll need to hit these with a drill. To keep the flapper from turning, hook a vice grip on the end that's sticking out. Drill off the heads. Once that's done, on the right hand side where the flapper bar comes out, you will see two spot welds holding on a cap. Hit them with a die grinder, hacksaw, drill, or something to get them removed. Then set it on its side, with that side down, hit the other end with bar stock pushing the rod outward. The cap that was spot welded should fall off. Then you'll need to put it over a hole so you can drive the rod out and be done with it. At first I thought the exhaust might be Titanium, but it turns out its stainless. Take it to your local welder and have the holes welded closed. Then put it back together. No problem"¦..
This will help you if you're changing out the whole exhaust system as far as removal of the header pipes go. Once you get your ECU flashed (I had mine done at AF1) the flapper is not in use anymore, which is fine by me. So, I decided to get rid of the flapper itself, and the actuator motor. With the ECU flash, you get no warning light when you remove the motor. I wanted the flapper out of the exhaust. I didn't want to find out that it got stuck in the closed position after removing the motor and cables. So, let the fun start. It's all easier than it looks, but you need some patience to figure out little things like how to remove the bodywork side panels. Reason for that is you have to remove the front two headers to pull them forward to get the rear collector off. (Make sure you order two new exhaust gaskets #852090) This sounds like a lot of work, but I think I had it all off in an hour and a half. Ok, back to the side panels. There are two push/pull tabs on the inside of the panel at the top. You just need to remove the rearward one. And the one on the lower area on the inside. They come out rather easily once you get a thin screwdriver in the groove to pop it open, and then it just pulls out. Then take the two stainless allen's off the front top of the radiator to remove the black cowl that goes around the top of the rad. My bike has aftermarket signal lights on there, so not wanting to unplug it all, I just duck taped them up out of the way. Then go to the bottom of the radiator and on the right lower side, there's a cir-clip that you just put a screwdriver blade in and twist it till the clip comes off. Then push the pin out that the cir-clip was attached to. You do this because the oil cooler stays in place, but the bottom of the rad is pushed forward so you can get to the header bolts. You then go to the left side of the rad, and remove the bottom hose to drain the rad fluid. Just pinch the clamp and it'll come off. I strongly suggest a pan under it. You'll need a hose clamp because the factory clamps aren't reusable. Once the hose is off, push the bottom of the rad forward. I use duck tape wrapped around the bottom mount, and then push it forward and tape it to something like the fork tube to hold it there. Do not hit the fins with anything! When working on the manifold nuts watch your clearance distance from the fins with your wrench or hands, anything! They bend if you breathe on the wrong! Now take the four header bolts off. 10mm. Then move to the rear and remove the endcan. It's held on by a strap bolt, clamp, and a rubber mount on the inside that you may not see until you've pulled on it ten times. Trust me on that one. Then remove the two locking nuts from the actuator cables and the 13mm nut holding the flapper mechanism in place and pull the crap off the collector. Then go forward and remove the motor. Two 8mm bolts hold that on. Unplug it from the harness, and tape up and zip tie the harness out of the way. I put two smaller bolts in to fill the exposed holes. That done, move to the other side and remove the springs that hold the exhaust sections together. There are three of them. You'll need a spring T wrench, or slide some wire (like coat hanger wire) over the hook and pull on it with locking pliers. Once you have them removed, you can now pull the front section forward, (the front headers have to come out of the exhaust flanges. That's why you need the exhaust gaskets) and the collector down to remove from the rear header, and reward to set the collector free. Now you have a clear shot at the insides of flapper-valve. There are two screws holding the actual flapper in place. They are welded. You'll need to hit these with a drill. To keep the flapper from turning, hook a vice grip on the end that's sticking out. Drill off the heads. Once that's done, on the right hand side where the flapper bar comes out, you will see two spot welds holding on a cap. Hit them with a die grinder, hacksaw, drill, or something to get them removed. Then set it on its side, with that side down, hit the other end with bar stock pushing the rod outward. The cap that was spot welded should fall off. Then you'll need to put it over a hole so you can drive the rod out and be done with it. At first I thought the exhaust might be Titanium, but it turns out its stainless. Take it to your local welder and have the holes welded closed. Then put it back together. No problem"¦..