Codec Clock Sync for Testing Circuits

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I wasn't sure where to post this so please let me know of any another forums that you might think is better.

I want to test and compare changes to analog circuits by using a codec to send a test signal through the input of the circuit being tested and then simultaneously record the output.

I have tried this with a PC and an M-Audio FastTrack USB. I can run a test twice to get two wav files and I wrote a C program to compare the files sample-by-sample and then write a new wav of the difference. So I can then view the .wav to see the difference. I can also listen to the difference of two circuits. Pretty interesting actually.

However, there's a problem. The samples are not aligned. They are off by several milliseconds. So it is clear that the DAC and ADC are not synchronized. At least they are not being instructed to start at the same time. I don't know if this is a software problem (I'm using a seemingly obsure but actually very useful program called DSSF3) or if the FastTrack is simply not capable of being instructed to use a common period.

Can anyone recommend software / hardware or some combination thereof so that I can digitally transmit a stimulus through an analog circuit and then record it's output after a fixed and completely reproducible number of samples?

Again, I suspect this an odd question so if there is another forum about software or recording interfaces I would appreciate a pointer.
 
Why you can't use one channel for recording the input signal and the other channel for recording the output signal?

I'm not trying to view the difference between the input and the output. I am trying to view the difference of the output before and after making a change to the device.

For example, if I have a Germanium transistor clipping circuit and I use a slow transistor like 1MHz, I might compare that to the output of the same circuit but with a fast transistor. Then I could "see" the difference rise time between the two transistors as a function of frequency or amplitude.
 
Just to follow up on this, I have a solution that seems to be working at the moment. There is a program called Audio DiffMaker. After a few missteps on my part using this program, it can align and compare two wav files quite effectively. A good stimulus wav is important. I wrote a C program just to generate a wav file of a series of sine wave pulses increasing in frequency by log 10. I also unchecked the gain adjustment. Then I got clean diffs.
 
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