R – iPhone – get duration of linear PCM audio file

Keep looking at those docs. In "Core Audio Essentials", the section "Core Audio Plug-ins: Audio Units and Codecs" notes that:

iPhone OS contains the recording codecs listed in Table 2-5. As you can see, neither MP3 nor AAC recording is available. This is due to the high CPU overhead, and consequent battery drain, of these formats.

Table 2-5 lists several formats, but as the text notes does not include the ones you're looking for. If you want those formats you'll have to bring your own encoder.

how many times are these returning true?

if (leftStereoSample2 > 32767)
leftStereoSample2 = 32767;
else if (leftStereoSample2 < -32768
leftStereoSample2 = -32768;

just because you are not clipping, (because you are forcing it not to) does not mean you wont get artifacts (distortion) etc when you truncate the waves like that. i would see how often that was happening.

core audio has mixers. smart people have written code to deal with this kind of stuff already, so we dont have to :) MultiChannelMixer is one that does stereo mixing. check it out.