Installed four new iridium NGKs. So far the misfire remains. Is there a good way to determine if a coil is failing? Is there a way to eliminate spark problems, that would point me to carburetor problems?
a spark problem is very abrupt, carb problems are a slower rumbling symptom.
Never tried it, so I don't know how well the bike runs on 3 cylinders, but one thing you could try is to remove one spark plug wire at a time, and run it into the problem RPM range and see if the issue goes away on one particular cylinder. If you can isolate it to one cylinder that's half the battle. Then you can swap coils and see if the miss follows the coil or the cylinder. Never had to do this, so I don't know if you can swap coils and keep the wires attached (preferred), or if you'll have to remove the wires, swap the coils, and reattach the wires. Then do the 3-cylinder test again. Based on the different coil/wire/cap combinations you should see a pattern in the failure and narrow down the cause. If you had marginal wire/coil/cap connections to begin with, and have to swap the wires around, there's even a possibility that you'll cure the problem while troubleshooting.
Also keep in mind that one coil fires two cylinders, so if you have a bad coil it may show the symptoms on both cylinders. And, if its missing on both cylinders it might seem more severe when you remove one of the plug wires from the other coil, since you'll have 2 bad and 1 good vs. 2 and 2. Conversely, if you remove one of the bad cylinders you'll have 2 good and 1 bad, so it might seem a little better in that case. Just speculating, I think its possible that the coil could be bad on only one cylinder instead of both, I don't know all their failure modes.
The professional way to troubleshoot a misfire is to put all 4 cylinders on a scope and the glitch will show up on the scope trace. If you have access to someone with a scope, that's the best approach.