I don't (yet) know of a better way to testing the coil pack than just swapping in a replacement and seeing if the behavior changes. I'm sure there's probably a better way, like measuring the output using a multimeter. Actually, you might want to have a multimeter handy to check the output of your alternator. Are you seeing a voltage sag around the affected RPMs?
As far a syncing carbs goes, I would recommend using a tool like the one Yermo
linked to. They're inexpensive enough, and you want a tool that you can trust to be accurate. The gold standard seems to be a Tecmate TS-72, but they are prohibitively expensive. When I was going through the process, I considered building one of these DIY digital sync tools. http://www.venturerider.org/forum/showthread.php?73158-Built-a-digital-carb-sync
The process is pretty straight forward. You're going to calibrate the tool so that the levels are all the same when they're plugged into one carb body, then connect the tubes across all the bodies and see if the levels are still the same at various RPMs.
You'll need to have the tank off because the way you adjust the balance is by turning the screws between the carb bodies. There are three screws, one between the left pair that adjusts 1 & 2 relative to each other, one between the right pair that adjusts 3 & 4 relative to each other, and one in the center that adjusts the left pair relative to the right pair. You want to start by adjusting each pair separately, then adjust the center to bring the left and right into sync. It will likely take a few iterations (and some patience) to get everything synced up nicely. It doesn't hurt to periodically re-calibrate the tool (sanity-check), especially if the what the tool is telling you doesn't match with what you're hearing from the engine. As it gets more in sync it should sound more smooth, more even.
As you get it into tune, try adjusting the idle speed screw (underneath the carb rail, between 2 & 3) to the lowest RPM where it still sounds smooth. Should be close to 1200 RPM I think. And I like to adjust the throttle using the throttle cable adjuster, it allows you to make small incremental changes and know that it's being held steady while you're taking a reading on the sync tool.
The easy way to create a vacuum leak is to pull the cap off of a vacuum port on one of the carb bodies. You can do that while the bike is running and instantly hear the difference, then plug it with your finger to control the size of the leak.