Removing the darker nights change might be hard. The mod isn't set up in pieces. If you are able to edit the appropriate file(s) you'd have an edited tWoS version without it. You'd really have to know your nuts and bolts. Perhaps a gamma adjustment and making use of the scope color filters would be enough?
It looks like all of the optional mods can be enabled at any time without issue. You can absolutely do this after installing tWoS but maybe in the middle of a patrol a few would have not flawless changes.
The automation menu is pretty simple. You choose a script from the left (2 columns) and press the > arrow to add it to the active list (3rd column). Highlight it and press "play" button and it will turn green. I recommend the 2-hour patrol fix loop for real navigation.
When on station the hydrophone search with 1-2 hour surface runs in between are excellent for finding contact without a lot of keyboard labor. There are many different ones; find your favorite!
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