Replacing the spark plugs and having the bike run OK for a while is a tipoff. A new (sharp edged) plug will fire at a lower voltage than older plugs.
Using the same plug wire to check all three coils was a good move. That eliminates one variable from the testing.
How did the spark look? A fat blue spark is what you want, so if you were getting a skinny yellow spark that's another indicator of low voltage on the coil secondaries.
I'd take a close look at the battery first thing since the igniters and coils can be sensitive to system voltage.
Check the battery fluid levels and top off with distilled water (tap water wrecks batteries) and then charge it fully. Wire brush the terminals and cable ends, grease them, re-connect and see how it runs. If you've got a volt meter check the battery voltage at full charge. It should read 13 volts with 13.2 volts as a no-load theoretical maximum.
The battery voltage will drop with load so you might want to check it with the ignition on and the engine not running. It should read about 12.5 volts and if it drops below twelve you should consider a new battery.
The "snap,snap" testing you did was good and seems to indicate a bad igniter but it's still possible you've got three weak coils. A fraction of a volt difference between the igniter outputs in combination with weak coils can give the same symptoms, so you're not out of the woods yet.
Also, since it's Memorial Day, remember to take a minute of silence at 3:00 p.m.for those who have given all for our freedom. (
http://www.remember.gov/)
If it wasn't for them we'd be riding German bikes...