You can move the crew around. The new thing in SH4 is that you get 3 crews in one that change watch at 8 hours automatically. But you can configure them as you like.
The no eyes thing... there's a fix here in the downloads section. Search for it. It worked for me.
The klaxon thing is a simple sound file. I think it's the Data\Sound\Dive Sequence.wav file. Replace with "Through Fire and Flames" by Dragonforce and you're set
The supermods are TMO (Trigger Maru) and RFB (Real Fleet Boat) with or without RSRD (Run Silent Run Deep) for the us side and OM (Operation Monsoon) for the german side. You can find OM in the "SH4 ATO MODS" section and TMO and RFB in the "Sh4 Fleet Boats Mod Workshop". Enjoy