Keep SPI/TWI master active?
You should keep them enabled.

SD cards require the /SS line to be toggled at certain times, to e.g. reset the SPI transfer to a known state, cut an otherwise longer transaction shorter, etc.  So you cannot leave it always asserted, it needs to be controlled correctly.

You will run into problems with SD performance.  It is hard to find exact specifications for all manufacterers, but most SD cards can go "out to lunch" for up to 250 ms while doing internal write cycles (which may include large erases, or sector remapping to balance load).  You'll find that while writes to the card will initially return in a few tens or hundreds of microseconds, once in a while (maybe every 30 seconds or so, depends highly on the card) the card will take a few tens to hundreds of milliseconds to complete the write.  This means you'll need the capability to buffer hundreds of accelerometer samples, so you'll have to be careful to ensure you have enough free SRAM in your AVR for that.  Or, add external buffer storage.  I've had great success with FRAM chips, due to the speed at which it can read and write single bytes.