found the stock filter just laying in the bottom of the air box - not connected!
Before you panic ....
How dirty was the air filter? I ask only to try to determine if it was off from the start, in which case it would be pretty clean, or if it fell off sometime between 1 and 120 miles. A picture of the filter might help if you can post one.
If still under warranty, absolutely bring this to the attention of the dealer, including a picture of the filter, as evidence of the problem.
They may wish to do a compression test, a valve adjustment, (I would recommend re-lapping the valves) and perhaps check the content of the oil and even inspect the cylinder walls with a scope. I would insist on it.
It may well be that the engine is fine, but you have to look to verify and protect yourself.