2 SPI Slaves with 2 different SPI modes on one Arduino Mega
For anyone who has a similar issue with the SPI Bus, SdFat library has a Software SPI option built in (example here).
You need to modify your SdFat/SdFatConfig.h file, but that is minimal. Once you have the microSD card module on a separate bus, it will not corrupt the main SPI Bus.
Switching the SD Card module to it's own bus rectified the issue. Keep in mind that Software SPI comes with a speed penalty.