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a) using Audacity, how might I detect these errors, and b) how might I correct them. I wanted to encode a bunch of killer samples, but I need to figure out how to get accurate samples from my equipment.
I use Cool Edit Pro, now called Adobe Audition, but I'm afraid I haven't ever used Audacity. CEP has a feature called "synchronize cursor across windows", which means that when you have several waves loaded, they all are represented on same time-basis, that is, using same time-axis zoom, and same zoomed area. This helps quite a bit on the process, but is not essential.
First thing you need to do is verify that samples are same phase. That can be done by looking at both waves on time domain, with low or no zoom, on some parts containing non-symmetrical shapes, and comparing similarity of those shapes "by eye". Of course, they must be same parts on both waves. Non symmetrical means that the part of the wave that is over zero is distinctively different from the part that is below zero. Look and compare at different parts of both waves, in order to verify that those shapes are similar, or are inverted vertically. If phase is inverted in one, just invert the whole sample so that phase is the same in both waves, and verify that shapes are now similar.
Now, once phase is the same in both samples, you must time-align both samples with precision. I believe ABC/HR Java tool can calculate time offset difference on two samples, so this might help you. However, I don't use it. I time-align samples also by hand, by zooming some characteristic part of one of the samples (some peak that is easily identifiable, for example), and then, locating that part in the other sample. Then, I calculate the difference in samples using the cursors (thanks to the fact that both samples are time-synchronized in CEP). Then I see which sample is delayed with respect to the other, and and delete the calculated nš of samples in it, so that the delay is reduced to zero. Another way of achieving this is deleting some samples "by eye" on the delayed sample, several times, until it is no more delayed with respect to the other. Ideally, this process should be done at last with a precision of just 1 sample, zooming the waves as needed, but if the precision is of a few samples if can be ok too.
Now, the level-align issue. For this, after some experimentation, I have found that the more reliable and easiest method is what follows. First, you need to create, with the time-aligned samples, two new wave files, one with both left channels of the two samples to level-align, and another with both right channels. I do this by simply using copy & paste on a new blank wave file (of the same freq. and nš of bits than the samples at issue). So, I create first the left-channels new wave file. Then, I perform a FFT (spectral view or "Frequency Analysis" in CEP) of this new sample. Then, I can see a frequency graph of both left and right channels of this new sample at same time, being those left and right channels the left channels of the two samples to align. In order to have a good picture of levels vs. frequency in both channels, I use logarithmic view ("linear view" not checked), a FFT size of 1024 points, a Blackmann, Blackmann-Harris or Hanning window (this doesn't matter much), and I average ("scan" in CEP) a portion of the wave with some loud content, in order to have an averaged, smoothed frequency graph. In case of castanets sample, I scanned the 4 castanets part of the sample. I use a dB range of around 40 dB or less, for a good visualization of small level differences. Then you should see that left and right channel graphs have nearly same shape, but being one of them displaced a few dBs of fractions of dB over the other. If they totally overlap, they are same level. However, for having best resolution of level differences I just take readings from the cursors at a several parts of the spectrum that are high amplitude, between say 100 and 5000 KHz, and just calculate the difference. Difference on those parts should be the same, or very similar. That difference is the level difference between both left channels of the samples, you must annotate it. If level difference is below or around 0.1 or even 0.2 dB, then it's ok, no corrections are needed. Then, repeat same process for right channels, and annotate difference. Of course, you must take note of which sample is louder, and such.
Here I post a screenshout of this last step. There's a 0.4 dB difference between both left channels of the samples at issue (in the graph, between left and righ channels). The reading is at 366 Hz.

Now, to correct for those differences, you must open the sample to correct, and amplify/attenuate level of its both channels (separately if needed) so that they compensate for the differences found. Best way to do this is to convert the sample to 32 bit, do gain (level) correction, and then convert back to 16 bith with dither. I use flat (no noiseshaping) dither, triangular pdf, and 0.9 or 1 bit of amplitude.
Of course, it's a good idea to save the wavs just after every step of correction is performed, so that you can go back if you need to.
So, the whole process may take somewhat for every sample processed, but once you have some practice, it takes less.
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Thank you very much for all your help with the samples, posting new ones, etc.

I just wanted to help, thanks.