I split passages in chunks of 40 questions so its roughly six passages per sitting. Since real MCAT has seven in 60 mins, I try to do EK's 40 questions (six passages) in approx 54 mins since they seem a bit longer. This way I get closer estimate of how many I can miss at the most.
Btw, EK 101 seems to have VERY few real humanities passages like those pertaining to arts or abstract philosophy which you see more on AAMC practice. EK has plenty of social science tho. Did anyone notice that or feel the same?