- Did you find any specific reason why you would have to use SD2? Theoretically, any SD should be ok. However, if I remember right, there may be some limitations / differences in SD interfaces on iMX6 (maybe something with maximum speed?). Try to search in documents or on internet.
If you like, you can try to boot up OpenRex from SATA and test your Wifi in the SD slot.
PS: For Wifi, you may want to consider also PCIE mini card slot - that is how we do it. PCIE Wifi may be faster than SD Wifi (I am not sure what would be difference in price). Also, I am not sure why you would like to connect SD1 - because you are planning to solder the Wifi chip down?
I'm also having trouble finding the SD1_CD, SD1_WP, and SD1_LCTL pins. Are these pins critical for booting from SD1?
- if you would like to use standard source code, I would recommend to connect CD and WP pins. If you do not connect them, you may need to go through source code to find how CD and WP are checked (in older kernels, I think some stuff was handled as GPIO - means CD and WP pins were not even configured as CD and WP pins, but maybe they have changed it in latest kernels).
IMPORTANT: If you would like to boot from an interface (e.g SD1), be sure you check table of default settings after reset - there is a table in datasheet, where they tell you what pins exactly you need to use to be able to boot up from specific interface. Find the table and check what pins you would need for SD1 to be able to boot from it.
Another wrinkle in integrating the new chip on their recommended ports is that it calls for using UART5_RTS [T6], which is used as USB_OTG_OC was just connected to a pullup resistor. Would using USB_OC as a UART pin mess with the functionality of the the USB_OTG? The last small issue is that that UART5_CTS [V5] called for by the WIFI chip is in conflict with PCIe_RSTn [V5]. Can any GPIO be used to drive PCIE_RSTn?
- these are very specific design questions which I would recommend to test before you implement them on the board. Try to wire up your wifi, use all the pins as you are planning to use them and test it. If I would be doing that design, I would also test it - if you swap some pins incorrectly, you may have problems to boot up or to use specific interface. It is always the best to test it, because even you may think, that theoretically something should work - it doesn't mean it will.