Went looking back and discovered that these connectors were ordered from Digikey because no one on Amazon had them. These are the items I ordered. Just make sure you do better math than me and order the right number of the crimp connectors. I didn’t order enough the first time and had to re-order a bunch more in order to finish all the wiring. All told, it cost me around $50 for what I ordered, but I now have enough connectors to complete 6 or 7 CNCs. If you order just what you need, you can probably get them all for around $20.
3 position connectors for the end stops: https://www.digikey.com/products/en?keywords=WM2901-ND
4 position connectors for the stepper motors: https://www.digikey.com/products/en?keywords=WM2902-ND
Socket crimp connectors: https://www.digikey.com/products/en?keywords=WM2512-ND