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I found the proper core.req on GT to make the new .lvl file but the only bug is that it's missing ingame menu sounds like beeps and clicks. This I cannot find a fix for. If anyone has a fix, please share.

I'm almost positive menu sounds are stored in common.lvl. Could you post the core.req though just to be sure?

I also copied some small sounds files into the project folder as instructed here by Ace in this thread, also where I got the core.req.

It all works fine expect the menu click and beep sounds.

You'll likely need these files:
ui_load_lp.wav
ui_planetzoom.wav
ui_menuMove.wav
ui_keyboardtype.wav
ui_menuBack.wav
ui_cancel.wav
brnbeep1.wav

in data_ABC\Sound\global\effects

If you open the retail core.lvl in Audacity you will hear some UI sounds in the first couple of seconds. You could split these from the file into new wav files since Pandemic didn't provide us with any sound files.

EDIT
I split the beginning from the core.lvl, the sounds still need to be separated and named.
http://www.mediafire.com/download/6z6m7 ... _22050.zip

Well I have no idea about how to removing the sounds from the core.lvl, so I picked up most of the sounds you listed from here http://www.gametoast.com/viewtopic.php?f=64&t=28297

I added them where you specified and the new core.lvl still does not present any menu sounds.
Here's the error log from the munge with shell, localize and sound checked;
I'm sure the things about shell movies don't matter. And for the rest I just don't know what any of means. Never did anything regarding sounds.

It works for me, I just munged with Common ticked. The munged core.lvl was a little larger than the retail one.
The only difference between my project and a default one is that i'm using the Fixed and improved munge files.

EDIT
Updated this post