For the RetroPie menu - check if you have a retropiemenu folder under the retropie-mount folder on the USB. If you don't, then re-install the retropiemenu package from the core packages section in the RetroPie setup script. Make sure you have your USB plugged-in.
For the 2nd problem - you'll have to be more specific: what does in game configurations can’t be saved ? The emulator configurations are not saved on the ROM folders.
The screen I used is a 128*128 screen so yours may be different. There is also the guide in my signature for ili9341 screens, you will see the similarities between the instructions, and get some idea of the wiring
@TheSwedenGuy When you configure input in emulationstation, it automatically create the retroarch-joypads/YOUR_JOYPAD_NAME.cfg file. Try to configure your joypad input in emulationstation again and look if the "retroarch-joypads" file will be created.
So I was never able to get the USB interface that i was using to work. I ended up buying a new one on Amazon and it worked great! I bought an Easyget 2 player zero delay generic game controller USB to Joystick for MAME & Raspberry Pi 1/2/3 retropie DIY projects. it was very easy to set up and worked instantly. Your arcade looks awesome, hope this helps, good luck!
Is the pi connected to a LAN? I'm asking it because you can connect to to it via SSH and investigate what is happening. Maybe your bro needs to configure port forwarding in his router to let you connect to his pi...