Corrections forthcoming to most of what you guys are mentioning. Other than the 50 cal AA gun. Are you guys encountering the failure to elevate on the early war conning towers? The full-size beasts, with the covered bridge and high sides on the cigarette deck?
As for the Balao and Tench, those are currently set to be able to be given early in the game, and as such will show with "old" gear. You lose your radar and other items on any new boat "upgrades" that you get, but the gear does eventually show up again. The way CapnScurvy has it set up now is due to the earlier reports of issues with the upgrade process not working correctly in previous version. One of the main problems with the guns is getting a new gun, but the player not crewing it prior to leaving on patrol. You would sometimes then lose the ability to crew the gun at all, and maybe the gun on the next boat. The way it is now, you will not encounter that problem, which also eliminated (near as testing could tell) issues with the deck gun swapping places on upgrades, and losing the crew spots for it... We might try to re-enable some of that, but I dunno... This is one of those "game quirks" areas we were hoping that meticulous date-checking would "fix". It reduced the issues, but did not eliminate them.