I had exactly the same condition on my 07 headlight lenses. Yamaha replaced them under/during the original 1-year warranty. The condition has not returned, even though I have continued to use exactly the same chemicals & polishes for cleaning the bike. IMO your problem is NOT related to any cleaning chemicals but is a manfacturing defect. That's not to say that IonBeam is wrong. Chemicals certainly can and do cause the same type failures. Yours however, looks hauntingly familiar to me.
As to the bulbs being the cause, my lenses "crazed" while running bone stock bulbs. Since replacing the lenses, I've run Philips Vision-Plus bulbs. I also ride with headlights on high-beam almost all the time.
Since I live in a warm climate area, I suspected the additional heat of high beam may have contributed to the crazing. I did notice that the crazing expanded much more rapidly in colder weather than warm. Subsequent discussions with lighting engineers led me to determine that the thermal stress of high-beam on the inside, combined with cold air rushing against the outside surface was causing enough physical stress on the lenses to accelerate the crazing. Maybe, perhaps???
One thing is for certain, the crazing will not stop. It will get worse. It will get so bad that it eventually penetrates to the outside surfaces too, where you will be able to feel it with a fingernail.
I added a set of CeeBailey headlight protectors to my steed, along with the Philips Vision-Plus bulbs. Two years and over 50,000 miles have passed since those original lenses were replaced. My headlight lenses look perfect.
Once again, it's only my opinion based on my limited personal experience. But I believe Yamaha had a "bad run" of headlight lenses in the late-'06 to early-'07 models. I'll be happy to speak with your local dealer and or Yamaha if they want to talk about it. Just shoot me a PM.