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If you have a scope you can connect it to an output pin (that say goes high with the 2nd timer interrupt) and observe the timing between the pwm signal and the start of an ADC read.
The datasheet for the micro is definitely your best friend. For me, its painfully slow doing a new project as I have to read the datasheet 20 times for it to sink in, but it can be rewarding too.
Another tip is if you are using a breadboard, keep all the high current stuff totally off-board, the mosfet, battery wires, atty wires, everything.