Ok, after some careful reading of the datasheet, I find I am no longer any smarter then I was before I started. I can't find anywhere in the datasheet to say in compare mode timer is reset on a match. It DOES say for the Special event trigger the timer is reset. So I suggest this:

Go back to SET mode (Special Event Trigger).
Enable interrupt on A/D conversion done.
Have the ISR do this:
toggle a pin (for debuging speed)
move A/D results to a variable for later use
Return from INT

With that done, several things are solved for you.