hey - don't know if the question is still out there, but on the subject of how do you synch up two sources for comparison:
I like to start both recording devices going without a source signal turned on. Then you switch on the source. This can be accomplished by pressing play on a cd player if that's the source, turning an FM tuner on, or turning your phantom power on if you're testing with mics. Makes the start points real easy to find. You don't even need to worry about the end points - most comparison programs will give you a result that tells you everything is identical but A is XX seconds longer than B. (I needed an efficient way of doing this when I did all that JB3 bit accuracy testing).