I heard he learned for 6 hours at a time. How many of these sessions did he have a day? Did he get up and stretch in the middle? What did he do during his breaks in between study sessions?
For some background on the life of the Vilna Gaon, we have an introduction to his commentary on the Shulchan Aruch (the ביאור הגר"א) that was written by his sons. It usually appears at the beginning of most modern prints of the Shulchan Aruch.
The section from page 15 (bottom section of the image) addresses your question re: the Gaon's daily routine.
It implies that he was learning non-stop aside from his breaks for rest. It says that he accepted upon himself not to sleep more than two hours per day and he would never sleep more than 30 minutes at a time. During that "sleep", his lips would whisper "halachos and agados". Three of those half-hour sleep sessions would be at night and one would be during the day.
Re: breaking for eating, it says on page 14 (top section of the image):
From the age of 13 and on......he would eat a morsel of bread the size of two olives (k'zeisim) soaked in water. He did that twice a day: evening and morning.