Nathan,
plug caps refer to the sparkplug wire boots, or connectors. If the boots (or caps, or connectors) are toast, they will have higher resistance and as a result the spark will be weaker (if it sparks at all). Same goes for wires and coils. But if only certain cylinders are doing that, wires and boots are the best guesses (changing the wires might mean replacing the coils, though).
As for your problems, I would clean the carbs with Yamaha carb cleaner, with the carbs on the bike. Just drain the bowls, fill them with a 3:1 ratio of gas and yamaha carb cleaner, kick twice with the ignition off, and wait 30 minutes. Drain bowls, repeat until the liquid you drain comes out clear. I did this on my bike and the bowls are shinny on the inside (I later opened them up to check the jets). Kicking the bike will draw some cleaner up the jets, but DO NOT RUN THE BIKE, as the cleaner has a very low octane rating (I think). One of the guys on the old forum (were I learned most of what I'm telling you) dipped his carbs in the yamaha cleaner and they came out shinny inside and out. Inside only was good enough for me, though
.
Checking your sparks might be a good idea, as upgrading my ignition helped a lot.
These are all guesses, by the way. It's definately (probably? maybe?) a combustion issue. Wether it's fuel related or spark related, that's a different story...
Good luck