You have to remove the gas tank, the air filter/element, then get underneath. Here are the steps I use.
Remove the fuel tank:
1. Remove the rider seat (2 Allen head screws)
2. Remove 2 screws at the front of the gas tank
3. Remove 1 long screw at the base of the gas tank (under the rider's seat).
4. Lift up the gas tank from the front.
5. Remove 2 breather hoses from the gas tank
6. Remove Fuel line from the fuel pump
7. Remove the fuel return line going to the fuel pump
8. Disconnect fuel pump connections (2 plugs).
A small amount of gas will drip from the fuel line when you disconnect it, so have some rags handy to soak it up.
Now you'll have to get to the air filter.
Removing the air filter:
1. Remove the bolt holding the front down. (I believe it's a 10mm)
2. Remove air intake hoses.
3. Remove 2 lines on the right side (from a rider's view)
4. Remove 1 plug and 1 line on the left side.
5. Lift up the air filter and set aside.
Now, there's a heat plate in there (it's made out of plastic). Undo the zip-ties and pull that sucker out. I left mine out for a while, but I wouldn't suggest that really. Underneath that you'll see the ignition coils.
Pull up the ignition coil (CAREFULLY! NOT at the wire, pull from the connection point and pull and twist. They should pop out.) ALSO! There is a recall on all 2003 R6's for the ignition coils, if you haven't had yours replaced, call a local Yamaha shop and give them the VIN number, they will replace them for free if they haven't been done already, when the bike heats up they can melt the ignition coil and cause them to arc out, leaving you S-O-L and your bike missing and acting up.)
Put a socket down in there with an extension, loosen them, then use a telescopic magnet to pull them out.
Assembly is the exact opposite.
-Sean
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Take it to a trained professional.
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