GIFs? Ouch. I can't easily pause a GIF easily to see settings, etc. Because it's a GIF and not a video - I can't tell your play speed, but in comparison to your mouse the character movement, dialogue, config menu screen all seem to be running much faster than should be at default settings.
Firstly - Have you edited save or configuration or any other files using an application outside of the game?
Secondly - You are correct the "CG Enhancement Mod" shouldn't be a problem. However, have you loaded a clean install without the mod (backing up your save files from the old install) to confirm that it isn't the problem? That would be the first step in troubleshooting. Always go to the most basic version of the application (preferably a clean install in a different directory).
Thirdly - I see you have modified at least one setting "Battle Animation Speed" from Normal to Faster. Again, that shouldn't be the problem. Nor should changing the speed of text display on the UI screen. However, running from a clean install with default options might give clue.
Fourthly - In your second GIF, the start up splash screen isn't displaying when you start using Game.exe. This is another huge flag. Some have reported this with other RPGM games (and we have seen similar reports of black screens here - but usually on Mac systems). If you have two (or laptop plus one) - have you disabled all but the first to see if you get same issue? Have you tried to enlarge the game window to full screen?
Finally - I don't know how deep into your directories you're playing the game from. Have you tried it from the root directory of the disc (C:\ or D:\) to see if similar problems occur?
Definitely a bug needing fixed for the Gym quest, I see it too in v0.4.1.
Go to a previous save to prior to your first going into the gym and load it, doing those days over again. If you aren't already doing so - save in a different save slot every time the game opens the save dialogue for you. You don't need to save unless the game prompts you to.