I'll try and answer to the best of my ability.
1. I'm using the Naughty Tribute Mod but I changed the settings while it was active and yes it was installed correctly as per the instructions on its page and it was working fine.
2. I tried Shift+G while on the black screen as well as tried holding down Shift while launching the game. Both did not work.
3. I changed the render option to "angle" mode instead of automatic and changed the framerate to 30 instead of default. I have a very OLD laptop (Intel i7 2630QM 2 GHz processor, 8GB DDR3 RAM, 2GB AMD Radeon 6770m GPU)
4. The preferences.rpy is the same as yours.
5. Since it was the same there was no editing required.
Thanks for your help so far and for being patient