Good job ! You don't need the Anvart_Stiebler_Turms patch; it is already part of NYGM, as is the CAM ship patch, i.e.
Stiebler's patch can be applied to any installation of SH3, hence the reason for instructions and files for things already in NYGM.
You'll also run into some conflicts applying some of the other mods you want to try.
That doesn't mean they can't be used, just be aware. Feel free to ask any questions at the time you try them.
And don't forget if you try any other GUI; you must use it or Hitman's. Don't have both in your mod list.
There are ways to merge conflicting mod files together to make things work and anything can usually be made to work with anything. It just may take a lot of editing work. Some to the point where it really isn't worth the effort.

But that's for another day. :)

Still working good, been trying various immersion/additional mods, noting and fixing conflicts here and there. A few things related to SH3Commander have got me curious. :hmmm:

1. As stated before I use Commander to launch the game. Occasionally, on startup loading the game will crash to desktop. I was wondering if the settings and stuff Commander does for you (captain name, U-number, and the game settings for e.g. randomized crush depth etc.) are still in effect if I launch the game after the crash without using Commander.

2. An interesting tip came up in Commander: "SH3 Commander simulates the effects of thermal layers by default. You can remove this feature by deleting the associated lines from "..\SH3 Commander\Cfg\Randomised events.cfg". Any knowledge about whether or not those effects, and any other possible stuff related to Randomised_events.cfg, work as intended within NYGM?

3. There is a Commander option under Time Compression for When receive radio report. I have set Max TC 1 for that, but it seems like radio messages/reports rarely if ever change the TC from e.g. a high value to something else. What gives?

1. No, if you start the game via it's .exe no Commander effects are in force.
You also don't want to do that when using Commander, it will mess things up. See the Commander documentation for details. Better to just keep trying to start the game via Commander. It will eventually.
2. Everything but the malfunctions/sabotage section of that file work as intended in NYGM.
3. That will only work when you are very close to a convoy and get a convoy report.
TC not dropping is another SH3 omission vs. something not working right in Commander.

Too bad about the radio reports!

I noticed something peculiar. When I am underwater and go to the hydrophone station and then leave it, a wooshing sound starts to emit from around the hydro/radio room direction, audible at least in the command room and in exterior view by the bow as far as I could tell. Then when surfacing there is very large and unnatural white foam/wave-crash emitting from the bow, which keeps on for a short while. I don't think I have noted that before, so maybe one of the additional mods I installed is to blame, although I am somewhat doubtful that they should be causing such things. It's a bit irritating, being abnormal and making it more difficult to hear close-by ship propellers. Whilst not a complete disaster I do want to get rid of it so I will be trying to look into that myself, if you have any ideas let me know.

Here's the activated mods list:
NYGM Tonnage War V2.5 - Stand Alone Version
NYGM3_New
NYGM3_6F
NYGM_2017A
IABLShipsforNYGM_New_Thomsen
MaGui F
MaGui F FIX for NYGM v2017A
optional-stopwatch with speed lines for MaGui
New_clearsky_clouds
Sh3_volumetric_clouds&fog_V2.2
EAX_Sound_Sim_S3
depth charge noise - Rev A - NYGM
Harbor Traffic Add-In
Haunting Atlantic Wind
real_depth_charge
SH3UboatEngine
Spirit of machines
1500 meter bearing overlay
ail Das Boot officers mod v2.19
Das Boot Clothes
Supplement to V16B1 (JSGME)
Stiebler4C_Addon_for_V16B1
EnvSimAct_10

I don't mess with the hydrophone station but I've never heard nor seen what you mention. I suspect one of the sound mods involved would be where to look.

Oh and fwiw, you don't need the clearsky clouds mod either; it is already in NYGM.
But it also won't hurt anything leaving as is.