ChristianStrahl: If you are using the GOG Galaxy Client I have a update for you, I just experienced the dreadful complicated and confusing way to set the start parameters up my self, so I give you a more specific instruction now in the hope this helps you out.

Setting startparameter via GOG Galaxy Client:
1. Select the list of installed games
2. Select the game you want to add the startparameter to
3. Click: Settings Button at the very top right next to the PLAY button
4. Select: Manage Installation
5. Select: Configure...
6. A new Dialog show have opened now, scroll down with the sidebar
7. Activate: Custom executables / Arguments and scroll down if you have to
8. A new section should appear, looking similar to the File 1 settings
9. At File 2, there is a Arguments field, enter there the following start parameters:
+set com_maxfps 120
10. Now make sure you select the hollow circle with the text () Default executable next to it
11. Click: The OK button and start the game

Also if you have not tried the SKIP Intro Mod yet, please do so:
https://www.moddb.com/games/star-trek-elite-force-ii/downloads/skip-intro-movies

You would be the first Person I know for which a technical issue with that magnitude with the game could not be resolved in almost 18 years

About the fov setting
STEF2 uses userfov cvar instead of fov, userfov will be restored.
So you can put seta userfov "96" in your cfg file or type in the game console and the game will always use it.