Clarification noted, but you still have to have an empty save folder before starting a new FotRSU version, and you still have to have LAA enabled prior to starting also. Not doing so can lead to corruption of the Save folder, which leads to a weird game. I cannot find a reason for a failure of the game to "upgrade" your boat previously, other than points score. There has to be at least four patrols, and at least one "excellent" patrol, as well as the other three being at least "average" before you qualify for a possible new boat or conning tower upgrade. You cannot have a "poor" showing on any of those, else the game knocks your rating way down. The way the game 'scores' and 'evaluates' a player's renown score and captain's rating is weird, strange and obtuse to say the least, but we cannot control that. If you didn't score enough in v0.80, that would be the factors involved. In v0.81, we lowered the "score" a player can accrue again. That will have to be reviewed further after more beta testing. As for the guns, those are date-based, and show-up for all players and all subs at the same time, considering the equipment that is valid for a given sub. The "S-boats" do not have much to be upgraded. As they were brought on-line out of storage during 1941, their 4" guns were removed and replaced by 3" ones. The 4" guns removed from the "S-boats" are what becomes available to the fleetboats later. Robbing Peter to pay Paul... I would guess (only a guess) Michael Wood, that the corrupted save with the Narwhal was due to not having LAA enabled, and the game (not your computer - the game) couldn't write correct data to the Save file. Not having an empty Save folder prior, whether you did or did not, also contributes to bad Saves... just sayin' - I can find nothing wrong with the first mission you did, and I tried three times with it, both in Career, and building it as a Single Mission. No issues. Something was messed-up in your game at that time, if a submerging to PD and surfacing did not get you the "Launch" prompt and / or icon.
