I can’t route your PCB traces for you directly, but here’s exactly how to wire in Flux per the documentation:

"To connect parts, hover over a part to reveal its terminals, then click on the white dots to begin routing mode. You don't need any tools. simply click where on the white dot to start wiring. To complete the connection, click on the terminal of the other element. Connecting parts While in wiring mode, you can also change the wire angle (elbow) direction of the route by pressing the “f” key. To cancel the routing mode, press the escape key. Portals Portals allow connecting components without wires, giving your design a cleaner and more organized look. A simple example part of a portal can be found here. To connect multiple portals together, type in the same designator for each one. Every portal provided with that designator will be connected to the PCB and simulation. If two or more portals are connected properly, you should see all of the connected portals turn blue, as shown here:" Source

If you want, I can review DRC/airwires after you route and confirm all nets (SPI, I2C, power, EN, INT, SD_CS) are fully connected.

components to be removed from the project