I gave you my list, but I see you added several more. I would get rid of SMMO, with TMO and other mods you should already have what it includes and it may even take away something as it's old..
You do want to run your other mods after RSRD, although you should get few overwrites, none I gave you effect traffic. I see you added some improved AI, not sure what that doe's, but that would overwrite TMO and maybe RSRD, so depends, but I wouldn't trust it with TMO. Main thing is to know what files are being overwritten, you have several I just don't know. I think Duc has a harder AI for TMO, but again RSRD will change crew settings. I just went in and edited mine to put harder crew ratings back over RSRD.
Truk redo is in RSRD, plus it may effect RSRD traffic location if the mod is different, I would nerf that.
Carlito's seafloor isn't in TMO, it changes the graphics., nor is smaller plants and rocks, you can see the difference.
Tread slowly....
TMO gives you about all the eye candy out there inside the sub, I know of nothing else, except the 3d radar mods, but that also is a working radar and nerfs other eye candy and use can't use the freecam inside the sub, unless it's been fixed since.
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