[BloodBorn]

hmmmmm.........i guess you haven't watched the animatrix.

a lot of things are explained there......for example;
how the war between humans and machines started and how the matrix was "created". The Machines captured humans and started searching for a way to be able to controll humans through their (hehe...our) simple brains. A lot of experiments were done on humans till they found all the right nerve impulses etc.
Or i like the "Last Transmission Of The Osiris" (i think it's called that) shows how the humans found out about the attack on Zion and in Enter The Matrix we can see that Ghost and Naiobi are the ones to retrieve the information about the attack.

you're 13th floor theory might be correct, i too got a bit suspicous when Neo started to charge up with an EMP and then fierd it at the sentinels.

There are a couple of things i think you have missed tho.......The architect said that there were 5 Matrix programs before the current one, but the war against the machines has been fought for over 100 years, which would make it a 600 year war considering that each program lasted for 100 years.

damn......this story is just getting better and better by the minute.