Pinyin

Is there a logical reason why the finals in zi, ci, si, zhi, chi, shi and ri are pronounced so differently from the other finals in the i collum?

Also, is there any correspondence between the way the pinyin chart is organized and the way sound are organized in Chinese? For example, are there Chinese dictionaries in which you can look up words by their phonetic sounds and, if so, are they organized in a similar manner to the pinyin chart?

Are there any books or articles that you would recommend that I read about this? I like to understand the logical structures behind language organization and usage, and at the moment Mandarin phonetics seems somewhat arbritary.