Yeah the main differences in in the lumbar holes, anchor placement and fairwater.
Than you have to decide on what time for each boat you want to depict and what other modifications where made and what paint scheme it has at that given time.
Lumbar holes differ between ship yards than as the war went on each sub would get modified for faster dive speeds.
Fairwaters got modified and chopped down, weapons would get replaced moved or omitted.
Also don't forget the flood openings on the bottom and the exaust pipes on the side as these where left off the model.
Deck storage tubes where often moved, added or removed.
Assorted other items would be added or moved, radar was upgraded.
The doors on the sides of the fairwater need to be removed since they are only on the museum boats to keep the public from entering and getting hurt.
Best places I have found for modifications are SubCommittee and AMP forums.
SubCommittee is by far the best site for info on the Fleetboat that I have found.
Sub Pirates in no longer readable unless you are a paying member.
Not that they ever had anytyhing of intrest to read anyway accept for a couple build ups.
SubCommittee has a section called the Fleetboat Dock that is just for Fleet Boats.
AMP has some aftermarket items in the works like accurate torpedo doors.
There are the AM parts mentioned that I posted a link to earlier also Nautilus Models Fairwater sets as well as laser cut wood decking (can't find the link) and PE detail sets and deck guns at White Ensign.
Eduard does PE for the Gato.
Almost all the WE and Eduard kit's can be found at Squadron.
Eric...