Claudio, I am no expert on the subject, but I will attempt to answer some of your questions from the little that I know on the subject.
A. Raphael Semmes was promoted Rear Admiral in February, 1865, and was never a commodore. I assume that you mean commander, which rank he held earlier in the war.
B. Page 145 of the William C. Davis volume, REBELS & YANKEES: THE COMMANDERS OF THE CIVIL WAR, shows colored representations of the Naval Officers ranks, and the shoulder straps are shown with sky blue backgrounds.
C. Not very sure on this one, but I would have assumed, because they were desk bound, that these officers would have been considered as staff officers.
E. Pilots and boatswains were not the same rank, though some boatswains did serve in that capacity. There seem to be some differences between a pilot's rating in the Confederate Navy, as opposed to that of the Union Navy. I certainly would like to see this particular subject researched further, as I consider it rather confusing.
F. According to the few xeroxed copies of pages from the REGISTER OF THE COMMISSIONED AND WARRANT OFFICERS OF THE NAVY OF THE CONFEDERATE STATES TO JANUARY 1, 1863, which I have in my possession, the rank of master's mate seems to have existed prior to November, 1862.
G. Assistant surgeons and assistant paymasters were commissioned ranks. [I definitely have to also include this one here to clear up some misconceptions spread by one so called expert: A SAILMAKER WAS MOST DEFINITELY NOT A COMMISSIONED RANK.]
Hope this little bit of data helps somewhat.