datalogging sampling frequency bottleneck
First, based on my experience with similar hardware, something about the sd card I/O stinks: it should be plenty fast enough. Using a class 4 (cheapo) sd card I've seen a 16mhz AVR do a FAT filesystem open for appending, write a new record of maybe 70 characters and close the file, all a few hundred times per second. This was with the Arduino "SD" library apparently written by Sparkfun in 2010 and improved by Adafruit sometime later.

Maybe the I/O library you're using is dog slow? Another possibility is that your SD card has a lot of files on it and something about directory (folder) traversal during an open is the bottleneck? (my experience is with just a few files on a given sd card)

But you could try buffering N samples so each sd card write records N samples.

If you do this, don't forget to "flush" any remaining samples when you go from "sampling" to "not sampling" modes, if that's possible. That is, if something is telling the thing 'start', then 'stop', part of the response to 'stop' is to get the N-m buffered samples written out to the sd card.