Hi Wildspear,
Mare Island was a Naval shipyard as mentioned previously and employed civil service people to build the boats under Naval supervision. Portsmouth Naval shipyard was the lead design shop for the Navy yards so MI used the PNSY design packages. The Gato class submarine was specified by the Navy Bureau of Ships and EB and Portsmouth created their own design packages. The differences were minor and mostly exterior. Things like limber hole size and number, and placement of the anchor are really the only ones we modelers are concerned about.
Here's my list of references:
Alden, John D., The Fleet Submarine in the U.S. Navy, 1979, United States Naval Institute, ISBN: 0-87021-187-0
Friedman, Norman, U.S. Submarines through 1945, 1995, United States Naval Institute, ISBN: 1-55750-263-3
Lott, Arnold S., LCdr, USN (Ret) and Sumrall, Robert F., HTC, USNR, USS Bowfin (SS287), 1975, Leeward Publications, ISBN 0-915268-05-1
Stern, Robert C., U.S. Subs in Action #2, 1983, Squadron/Signal Publications, ISBN: 0-89747-085-0
Stern, Robert C., Gato-Class Submarines in Action #28, 2006, Squadron/Signal Publications, ISBN: 0-89747-509-7
Wiper, Steve, United States Navy Gato Type Fleet Submarines, Warship Pictorial #28, December 2006, Classic Warships Publishing, ISBN: 0-9745687-7-5
The Fleet Type Submarine, NAVPERS 16160, June 1946,
www.Periscope.com, ISBN: 1-4116-7753-6
The Fleet Type Submarine Online Submarine Periscope Manual, NAVPERS 16165, June 1946, available at
www.maritime.org/fleetsub/pscope/ Fleet Submarines of World War Two, 1988, The Floating Drydock, ISBN: 0-933126-72-7
Plan Book, Gato & Balo Class Submarines, 1990, The Floating Drydock, ISBN: 0-944055-06-0
U.S.S. Cod WWII Submarine Memorial, Photo Museum Guide, 1999, Oxford Museum Press, Inc., ISBN: 1-930127-01-4
Another very good source of information is The Floating Drydock,
http://www.floatingdrydock.com/. Tom has a number of the design documents generated by EB and PNSY and they are excellent for identifying the details. Look under his "Bu Plans" section. As has also been mentioned you must determine the year in the Silversides's career that you want to model as the boats became as unique as fingerprints over time due to modifications and overhauls. The deck guns she carried also changed a number of times during the war.
I went aboard the Silversides a few times when she was at the Navy pier in Chicago in the late '60s. Last year I got a piece of her teak deck for making a contribution to her refurbishing effort.
A couple of other things regardless of which boat or timeframe you pick: Remove the hatches on the fairwater (those were open arches) and remove the broom ( not normally displayed). Revell copied the Cobia too literally. Most museum boats have something covering the arches to prevent visitors from getting underneath the fairwater because of liability issues. The grills should go too if you are not modeling the boat as it came out of the yards brand new.
Have fun.