Reverse your Y motor direction by changing S1 to S0 or vice versa in your M569 P1 command. If it then homes in the wrong direction, you will need to change your homey.g and homeall.g files to home in the -Y direction instead of +Y.
The repair cost won't be known until your board is examined. If you didn't apply 12V or 24V power to it, then I think the worst that can have happened is that 5V got fed to the 3.3V rail (which would account for the SD card failing). In that case the processor and the WiFi module have likely failed, but probably nothing else because the other components connected to 3.3V (e.g. stepper drivers) would not be damaged by 5V.