Sorry, but I'm still not clear...
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However, when a offset of +1 or -1 is applied, the troughs disappear.
How do you know that? What does the file
sound like? Noise?
Of course, you can't improve quality by shifting bytes or frames... If so, the MP3 developers (who are smarter than most of us) would have that built in already.

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So actually i wish to perform this and plot it out myself.. However as i am new to this, im having a lot of problems now..
Do you know any programming? This looks like programming to me... You can shift
samples in an audio editor... You can open an MP3 (decode it) shift the samples and re-save it (re-encode it). But, that wont affect the spectrum, and I don't think that's what you're trying to do.
I
think I understand what you're doing with WAV files... If you've got a 16-bit stereo file, each sample is 4 bytes. For a +1 sample shift, you "right shift" all of the audio data by 4 bytes, and presumably fill the first 4 bytes (of audio data) with zero?
Is that what you're doing?That will work fine with WAV files, and you have simply added one sample of silence at the beginning and time-shifted the audio. (Of course, you should either adjust the header for the new length or throw away the last sample.)
If you try that with MP3 files, I don't know what will happen... My
guess is that you will simply corrupt the 1st frame. As pdq said, the "raw samples" don't exist in the MP3 file. The samples don't exist until the file is decoded... Think about this: There are more samples than there are bytes in the file.
You could shift by a whole frame, and thereby create a time-shift (bigger than one sample), but this will not affect the spectrum.