Already a few old posts on the subject, but some files I couldn't find so I made another little list.
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Found some new files to change in s3dspy
I didn't delete the files I just made new ones with sounds I can handle and a lot quieter and replaced them for consistency.
there are three files for the loud boom in lava storm
one was already found in a previous post
snd11.pfs > thunder_rolling.wav
another one that loops with it is
snd2.pfs > test.wav replace with something sounds more quiet.
There is still one more that I have not found yet
EDIT:
Found the third lava storm loud booming sound file.
snd11.pfs stomp_02.wav
bags
snd2.pfs > itemclth.wave
chests
snd2.pfs > chest_cl.wav and chest_op.wav
rain loop
snd2.pfs > rainloop.wav
Thunder
snd2.pfs > thunder1.wav and thunder2.wav
snd14.pfs > thunder_distant_lp.wav