The first thing I would do, is charge the batteries and perform a load test on them. Some batteries don't last long and stop holding a charge. A defective battery can blow a rectifier. When hooked together through a battery switch, a bad one can pull the good one down. It's best to have an isolator so that you can charge both but current won't flow from one to the other.
After you charge the battery, take a voltage reading with a good digital voltmeter. Record the voltage and then start the engine. Take a second reading while the engine is running. This reading should be at least one volt more, if not one and a half more.
The most important thing is that if your engine is an '06, it's under warranty. Take it to the dealer so you don't give him grounds to deny a claim. You paid good money for it. You should also get a Yamaha factory service manual. It's saved me lot's of money when I do my own work.
Good luck
Here's a good digital, inexpensive tester.
http://www.harborfreight.com/cpi/cta...emnumber=90250