Hmm... Maybe try using those mods that are GWX, in the mix, as being activated 1st... with the SH4 effects, then the lifeboats, firs. then see how that goes... then add in the ASN mod test that.. then followed up by the torp damages mod, lastly... testing SH3, with each step of adding in mods, after activating the main GWX mods altogether 1stly..
With the GWX mods themselves... as far as I know of.. shouldn't be causing you issues.
So, that leaves either the rest of the mods not being in a certain order to work right.. or is 1 of those left, that are NOT GWX mods.. causing the issue.
1 other thing I can think of here.. is did you have some other mod, added in, then taken out... If so, did you delete & reset up SH3 options in game, in a 1st run after doing a delete of the save game folder.?
Not doing that, after removing out a mod, can & will cause issues.. that much I do know from what I've seen of others reporting various issues after removing a mod & not deleting the game save folder.
M. M.