I would have programmed from scratch using PIT0 from kinetis documentation. (could not find intervaltimer on my TD installation, so I cannot confirm if this is OK for T3.x) Unfortunately the PJRC website examples is full of Teensy2 examples.
...
static Queue queue1(sizeof(int), 50000); // Instantiate queue
static const int SD_CLASTER_SIZE = 512;
while((!queue1.isEmpty()) && (queue1.getCount() > SD_CLASTER_SIZE)){
queue1.pop(&incoming);
rawFile.write(incoming);
}
rawFile.flush();
...