I am not as familiar with SH5 as I am with SH4 (which really is not that much either), but there are several things in common between the SH series games. Number one suggestion is to read vdr1981's install instructions for TWoS, "The_Wolves_of_Steel_2_x_Install_instructions. pdf" (the name changes with each version of the mod), found in the TWoS mod package (the "The Wolves of Steel - Documentation" folder). He goes through the steps necessary as prep for the install, and then the install itself. You have to have v1.2 of the game. If you have the disk version of the game, you might not have the update. Be sure of that. Start with a "clean" installation of the game, update to v1.2. He goes through other points you need to do prior to the mod's activation (which is done with an installation package).
However, one of the biggest issues with the SH series of games is what MS did with Windows with the introduction of the Vista version of the OS, and that is the "protection" of what they call "system" folders and files. Windows will roll-back most of the changes you or JSGME would make to files or folders in the "Program Files" folders. This is accomplished with User Access Control (UAC) and other "technologies" now in the 'modern' OS, including Win10. If you are installed in "C:\Program Files (x86)\" (or the plain "Program Files" folder if a 32-bit version of Windows), you will have issues when applying mods, since the cfg files and others are set back to what they were for the game install, and then you end up with a mix of the Stock game, and TWoS.
You also want to match your video stream from display monitor to game, as well as set other items. Prior to activating / installing TWoS, you should run through the properties for the game. Navigate into your install folder (ie: "C:\Games \Ubisoft \Silent Hunter 5") and select the "SH5.exe" file. Right-click on the file, and from the context menu displayed, choose "Properties" at the bottom of the list. Click on the "Compatibility" tab of the resulting "SH5.exe Properties" window. Depending upon your computer and Windows OS, you might have to select the "Run this program in compatibility mode for:" and set that to "Windows 7". Near the bottom is "Run this program as an administrator", which you definitely want to click. You can also use the "Change the settings for all users" button, and set these there. There are severeal differences between the various versions of Windows from Win7 through Win10, but notice the "high DPI" setting, which might have to adjusted later. "OK" your way out of everything for now though. When you go to run the TWoS installation package, right-click on it and choose "Run as an administrator" from the pop-up menu.
If your monitor's "Native" resolution is 1920x1080 (as an example), you should set Windows to match that, which will show as "1920 x 1080 (recommended)", and you should use that for Windows. Once in the game, click on the Options menu, then the Graphic Settings tab, and make certain the game is set to that same setting. You can experiment with that after you get TWoS running. When you activate the mod, be sure you select a correct path to the game, and - you have to step through the Generic File Patcher properly. Pay close attention to what you do here, and make certain all goes as noted by vdr1981. I would recommend to NOT add optional mods to TWoS just yet. Make certain it is functioning correctly first. When you do attempt to run the mod, you will get the usual SH5 Ubisoft updates etc., and once you get through all of that, you should get the TWoS title splash screen. After that, it will take a while to load to the menu (as you are aware). Try a new campaign (career) again. Save the game there. Do NOT go onto the boat. Save the game and exit to the Main Menu. Now you can Load the saved game, and go from there. vdr1981 notes that you have to do this step for each new career, or when advancing to the next chapter.
Someone else will likely have more / better info for you.
