In the root folder for the game, there is a "Large Address Aware2_0_4.exe" that you can run. It will start in Basic Mode. Click the ellipse button [...] for Step 1, and select "sh4.exe" and click on "Open", which will put its path in the Step 1 box. Then put a tick mark in the Step 2 box with a mouse-click. Click "Save" in Step 3. If the tick mark is already set in Step 2, it's good to go.
Now, there is an issue with the sonar station in SH4, and I do not recall when CapnScurvy fixed that in FotRSU. Other things that can contribute to issues like that, are using old Save data from previous mods or Stock game play, which can cross-contaminate the game. Also, mixing mods not compatible with FotRSU.