Okay, so i notice a few things before i could even really try it out.
So you wrote that we should use any version of Mupen64Plus that is not Mupen64Plus-nx.

I normally use mupen64plus-gui from here:
https://github.com/m64p/mupen64plus-gui
With this one i can´t even get to the point of launching any game. Mupen gives me this error:
"Couldn´t load core library, please set the path in settings."
I have that already set, and it´s pointing at it´s dll in the correct folder, but it seems it wants to simply ignore it, which is sad cause i really want to use this Frontend.

The second i use is M64Py from:
http://m64py.sourceforge.net/
I can get it to load the Game as it should. Except nothing i change in the config (MouseInput.wren) does anything. I changed the FOV to 90, FPS to 60 or MAX. But nothing changed. I restarted the Emu and Game multiple times. I still noticed the inbuilt FPS Counter was still on 30 FPS so i think i am doing something wrong?

This has been superseded by the mod in this thread

What is this?
Knockoff Turok 3 EX?
This is NOT a PC port. This is merely a collection of memory hacks that have sprung from my reverse engineering utilizing my fork of Mupen64Plus

What does this give you?

• Mouse input with customizable look-sensitivity
• 60 FPS mode
• Custom FOV

What problem does this solve?
This completely bypasses the joystick, so you are not limited to the game's interpretation of the stick input. You are not limited to the -128-127 range on either axis.
Furthermore, who doesn't want to play at 60 FPS?

Cool. How do I get it?
Download any version of Mupen64Plus that is not Mupen64Plus-nx!!
Download and extract this into the root directory of Mupen64. This should replace "mupen64plus.dll", and you should see a new folder called "scripts."
That's it, run Turok 3 in Mupen!

Note that for proper keyboard controls, you will have to configure the input of Mupen to use your desired buttons. I will not go over how to do that but do highly suggest sharing your configurations when you get something that you like.

How do I configure the options?
In the Mupen64Plus directory, navigate to ./scripts/Turok 3 - Shadow of Oblivion (U) [!]/ and edit MouseInput.wren with your text editor of choice. The options have comments describing their relevance.

Bugs

• If you get an issue related to the input plugin, replace it with this
• When playing at 60 fps, some levels cannot be completed due to some scaling issues.
• Climbing ladders is inconsistent and sometimes buggy.
• You cannot modify the FOV when running in dynarec mode

Other notes
You can press  HOME to lock/unlock the mouse
If you fancy learning a high level scripting language, you can use what I have already set up to make more memory hacks that may do a plethora of things.

Special thanks to Kaiser