References on the MP3 encoding algorithm Does anybody have a reference describing the MP3 algorithm in a step-by-step manner and clear to understand?  

These references were a little bit confusing:  


Audio compression using modified discrete cosine transform,The MP3 Coding Standard, Joebert S. Jacaba, 2001
The Theory Behind Mp3, Rassol Raissi, 2002


I am willing to encode a bitstream to MP3 after reading the reference that you introduce, manually, for a complete understanding of the procedure.
A compression standard is a quite delicate thing, that took years to develop and tune. I suggest Analysis of the MPEG-1 Layer III (MP3) Algorithm Using MATLAB, 2012 by Jayaraman J. Thiagarajan and Andreas Spanias. After a general overview, it leads you step by step though the different blocks of the whole scheme, providing some Matlab code for each of them.