Well, here is the mod list I've been testing with fitzcarraldo
Generic Mod Enabler - v2.6.0.157
[C:\Games\FotRSUv17\MODS]
100_FalloftheRisingSun_Ultimate_v1.7
AddInModzPak_17
EAX_SoundSim_FOTRSU_1.7
Fleetboat_Interior-Officers_Quarters_FOTRSU_v1.46_EN
FIOQ_FotRSU_Patch
I have been through Conning Tower 1, 2, 3 & 4, and have not found any issues in the Gato. In that list, the "AddInModzPak_17" isn't really a mod, but just the Pack that I then pull the bottom "FIOQ_FotRSU_Patch" out of the Extras / AddInModzPak folder and put in MODS for activation. If you could, post your mod list,
Sent you a dm, with My modz list that I was working with... before I culled out Canonincus' peri wake splash mod and I'll try to match it. I don't know what mod MM is talking about with the splash
(of which I posted definitive info on that mod & where to locate said mod... 
), but if you guys could clear that up and point us to it, we might be able to swing it.
already done... There are a few mods out there that should most likely be compatible, but we have not tested them as of yet. I am not certain about Webster's clearer water mod
This mod, sets it to less fog, & clearer waters, taking out the... murkiness.. so that the skipper, can see their own boat, underwater... that's it. To the best of My recall... it does nothing with the AI behaviors, sensors or anything else related to that behavior... 
as near as I can tell of, at any rate... since, since I do perceive a change in escort behavior - but it might be my imagination. We have to do the "scientific" on it now, under a controlled situation to actually "test" it. There was another one we were going to do, but my mind is misplacing it just now - the eggnog turned on me the other day, I do believe...
- that's my excuse, and i'm sticking to it!
Couple of other things to look at, is an external view of your boat. Do you have a conning tower on the boat? You will see the scopes going up and down when that happens, and you won't be able to use F3 and "O" with that situation.
as for external view.. that was just dandy, on My end... scopes were normal, Yes... there was a conning tower, virginia... erhm.... uhm.... sorry... 
propbeanie... 
The issue for Me, & am certain the issues fitz noted, were interior... for whatever reasons. fritz, is of the opinion that it was the .dat file in the peri wake splash mod, that was the cause... am thinking that could well be the culprit... but... no way to confirm since .dat files... are NOT My forte... gimme a .cfg or the like & I'll rip through it, no sweat... even the menu.ini, though... am loathe to dink about too much in there... as it's more.. trickier than .cfg's, to Me... at least. I know My strengths & limitations... I'm not certain though if you wouldn't just CTD if you have vickers03's FIOQ enabled and end up with a bad conn assignment though, since the conn, control room, and Officer's Country are all connected now, which is why the F9 won't take you to the conning tower now. But let us know your mod list, and the date you're sailing with the Gato
For Me, t'was the Sargo, (USS Seawolf (SS197? I think is her SS #... as for the date, was 09/12/41... 2 days after Pearl being attacked... & outta Manilla. Ugh... got used to using f9, to go to the sonar/radar area... blast it all... 
was hoping that it could be worked out with vick's FI:OQ mod, that would be able to be done... like the interior view... though ahh well... ). Thanks!
PS Edit: I just happened to think - the interior could not care less whether or not a conning tower is placed properly or not on the 3D submarine... the "Interior" of the boat has nothing whatsoever to do with the "Exterior"... but if you do not have a conning tower showing on the external view fitzcarraldo, that would explain the lack of function for the periscope controls, and the up / down craziness in the interior of the "conning tower"... As to why you would not be assigned a conning tower, I don't know. UPC file issue, which is altered by the interior mod could be one source. Be sure you delete the Save folder, and try again, if nothing else. This mod is NOT backwards compatible with earlier versions of itself due to all of the submarine changes and additions.