High Speed Data Acquisition with SD Card Write
Within the TimerA ISR, data is collected from all the sensors. This takes approximately 1 millisecond


This could work fine, but why don't just start an SPI DMA Transfer in your timer? These beefy Cortex M4Fs usually have multiple DMA channels, the core is free to do other things (like finishing the SD card transfer one ms sooner) or to sleep, saving power.