You could be dropping voltage between the battery and the coils. With the key on, engine not running, measure the voltage between the positive terminal of the battery and the positive terminal of each coil. There's usually a pretty appreciable drop since the power has to go through the main fuse, key switch, kill switch, and then to the coils.
If this is your problem, it can be eliminated with a single relay and a few feet of wire. You'll basically be using the current "hot" wire that feeds the coils to engage the relay. A wire straight from the battery terminal will go through the contacts of the relay and now feed the power to the coils (through a fuse, of course).
My bike was dropping over a volt at idle and a volt-and-a-half above 2000 rpm before. Now with the relay installed, there is no measurable voltage drop and idle is much smoother, plugs last much longer (current set is over 2 years old) and my gas mileage has improved.