Good point, I think I confused Timer 1 with Timer 0.
So...the point of Timer 1 is just to generate a variable frequency waveform on pin 9? If so I think the code is overly complicated since pin 9 is OC1A and you can just drive this pin directly by connecting up the output compare through the TCCR1A register.
Anyways...you say that code works so no point picking on it.
I can't see why you wouldn't be getting A/D interrupts based on Timer 0. Perhaps put together a simpler sketch that just tests this one behavior. This will be easier to play with, read, and debug.
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The Gadget Shield: accelerometer, RGB LED, IR transmit/receive, speaker, microphone, light sensor, potentiometer, pushbuttons