I have a question about time in the Matrix. I fully understand the movies, and the meaning of the meeting with the architect. The one thing I don't understand is the passage of time in the Matrix its self.

Time is an illusion, see below.

claims that they've been fighting the machines for over 100 years (I want to say 120 years or something close to that). Regardless, how did these years get passed in the virtual reality of the Matrix?

What's to say that time in the matrix is equivalent to time in the 'real world'?

When Neo is pulled out, it's 1999 ("the peak of [our] civilization"). One possibility is that it is always 1999. How does this work and still allow for a life cycle?

If the Matrix can be rebooted, then it's possible to concieve that it's only *ever* 1999. The more live bodies at that time may have been conducive to the harvesting systems employed by the machines. Although that raises an interesting issue of why there couldn't be specific areas doing one thing separately to the others. Like a research lab, to fine tune the matrix elements to enhance crop output.
If the matrix can be re-arranged, then it would be possible to re-insert people into older instantiations in the matrix. Same sh1t different buck3t.

ps - the way I understand it, Morpheus was wrong in the first film, and it isn't anywhere near 2199 at the time they release Neo. If there have been 6 versions of the Matrix (7, including the utopian one), then it is probably closer to 2799. Am I thinking correctly here?

"No-one really knows for sure". if the matrix has been continually re-booting, then humans have actually lost track of the outside world.
I don't understand how the 'real world' people would get into Zion and not pass down any existing folk lore about the previous people in the matrix. Unless there is no 'real world' that we know of.

Why didn't they use cows?