I never said that your theory was wrong except for the Way stations.
Perhaps we were on shield worlds, or perhaps some Forerunners did survive, but were blasted back to the time of the Cro-Magnon. Perhaps we evolved from the other bi-pedal race on Earth. Hell, perhaps some Forerunners created us in a lab, set us down on Earth, and left. I never said that I believed that none of the Forerunners survived, I was playing Devil's Advocate, unless you've never heard of that.
Perhaps they constructed the Portal earlier on, to allow easier travel, from the Ark to Earth. For all we know, they could travel through time, and foresaw the finding of the Flood by use.