With those exhaust and intake mods, you will have to adjust the idle screws. This is a touchy feely affair. You need the bike at operating temperature. The screws should be adjusted individually. Some fellows short out a cylinder and adjust one running cylinder at a time. If you do it this way, make sure you ground the high tension lead securely to the block. I keep both cylinders running.
Adjustment - Simply turn one screw in until the engine begins to slow down then turn the screw out slowly noting an improvement in engine rpm, then continue to turn out until the engine slows down again. I then find the halfway point. Adjust the other side the same way. You might have to do this several times. You should then note the position of each screw by turning them in until they lightly seat counting the turns. The number of turns out each screw has doesn't necessarily have to be the same. Make sure you don't have any vacuum leaks in the intake system (check the squirrel condoms and intake manifold rubber boots). You should balance the carbs also after this is done.
Another item to address is the needle height. With stock needles you will probably need to shim each with 1 or 2 shims. This is a relatively quick process that is outlined in the tech vault or on Dinqua's website.
