More quick thoughts: 
    As I mentioned, I did not adjust the target strength calculations for variations in the temperature at the transducer. I ran a quick check and found that for wa3,wa4 and wa5 that the transducer temperatures (degC) varied by
wa4: 11.5 to 15.0,  wa3: 10.8 to  14.14  wa5: 11.3 to 14.4

Please check my calculations yourself with the equations, but for a quick calculation I found the following. 

If a change in temperature is inserted into the software so that temperature goes from 10.8 to 15.0, the target strength is increased by less than .1 dB.

I also used a constant sound velocity for all scattering layers. Changing the sound velocity from 1543 m/s to 1501 m/s will increase the target strength by about .12 dB. 

The greatest change appears to be from variation in the power into the water. For these three deployments where Vs (volts) = .17 * Vs (counts) I found the following range in values in volts:
wa4: 34.3 to 30.0  wa3: 36.5 to 31.9  wa5: 36.8 to 31.2

From the equations, a change in voltage from 37.0 volts to 30.0 volts would increase the target strength value by about 2.2 dB. This means that you can expect the target strengths that I reported to have a 1 to 2 dB decrease in target strength measured value (from the beginning to end of the deployment) that is not real. I think I have the sign correct, but you should check this. Although I indicated in my technical memorandum that I used a mean voltage for each deployment, I stopped doing this as it did not effect my identification of the location of the surface. 
However, If I have my signs correct, the mean voltage for wa3 is about 2dB greater than for wa4.  Since this was not adjusted for in my processing, wa4 should have had target strengths .6 to .7 dB greater than I have reported with respect to wa3. That again is if I have my signs correct. Unfortunately this appears to be in the opposite direction that the wa4 profiles in prof_ref80m_all.gif should probably be shifted. 

In any case, it appears after a quick look at the equations, that determining the background reference noise for the instruments has the greatest effect on the target strength values. 


Regards, Tricia