Based on my research, I will try to answer as many of your questions as I can:

A. Yes to the 5 stripes and 5 stars for Semmes. Based on the CSN uniform regs (amended in 1863), he would have been entitled to wear such. The 4 stripers were actually flag-officers, not Commodores. Commodore is a title in the CSN, not a rank. This title was given to a senior captain over a naval station, naval yard or a fleet of ships.

B. The background of the shoulder boards would have been a light blue. The loop is questionable as it referred to a line officer not a staff officer but this would depend on the officer as many line officers ended up over bureaus in Richmond during the war.

C. No

D. Regs don't indicate such but they probably had them.

E. Pilot was an officer but I am unsure if it was warrant or commission

F. Probably the uniform of a warrant officer. Remember also that there were warranted and unwarranted Master's Mates.

G. Not really sure but I will consult my information and post further on this item. I think they were equal to Masters.