I've been lurking on the forums for a while now and figured it's finally time to start my own build. This will be for a formal 10-week engineering class project so I'm looking to go as in-depth as possible rather than just following guides or using kits. Notably, I'm looking to 3D print my own case and custom design my own button PCB.
Does anyone have any advice regarding what the best PCB software would be to learn and how to implement button traces? For the buttons themselves, I'm assuming I can just use any rubber pad buttons from a spare controller, but are there any commonly used on the forums?
Here are the rest of my parts; feedback would be much appreciated

Pi Zero W (https://www.adafruit.com/product/3400)
2500mAh Lipo Battery (https://www.adafruit.com/product/328)
JST Extension Cable (https://www.adafruit.com/product/1131)
3.5mm Headphone Jack (https://www.adafruit.com/product/1699)
8 ohm 0.5W Speaker (https://www.adafruit.com/product/1890)
I2S 3W Class D Amplifier (MAX98357A) (https://www.adafruit.com/product/3006)
PowerBoost 1000 Charging Board (https://www.adafruit.com/product/2465)
USB Type A Female Breakout (https://www.sparkfun.com/products/12700)
Camble's Safe Shutdown Board (https://sudomod.com/forum/viewtopic.php?f=3&t=2260)
Gearbest 3.5 inch TFT LCD Display (https://www.gearbest.com/development-bo ... 29447.html)