I write for that i know. the ds1302 rtc can't manage ms, only seconds. Try with linuk kernel if any function,(time fox example support ms)
Foxboard can drive GPIO port in output with kernel driver at about 155-160 khz, i think that it can read at the same frequency, keep in mind the operation between your reads functions. There are some type of accelerometer, in spi, i2c etc interface... The ram partition is mount in /var. all others directory are in flash: look at http://foxlx.acmesystems.it/?id=14, you can read: "Be aware that the /mnt/flash directory is mounted on a FLASH memory that can only be written a finite number of times (about 100K). Please don't save counters, logs or other frequently refreshed files in this directory but use /var directory instead that is implemented in RAM memory. All the boards broken with this method usually can't be reflashed and will be considered out of terms of warranty."
