To log 1000 samples per second requires a totally different technique than your sketch.
I suggest you look at example sketches in fastLoggerBeta20110802.zip here Google Code Archive - Long-term storage for Google Code Project Hosting..
Forget advice like 512 byte buffers unless you are doing raw writes to the SD.
The big problem is that a write to a file on an SD can take 200 milliseconds. You must capture data while the SD write is in progress. This means interrupts, probably using timers, and cleaver buffering schemes.