Oh God this feels like deja-vu! Check out the thread that still appears to be alive on this forum: 'Alien prequel script - Jon Spaihts', started by user 'samH3LL'.
In that thread there are links to two known Jon Spaihts works: 'Passengers' and 'Shadow-19'. I remember scanning through them at the time to find any tell-tale clues and a possible correlation with the Harvest script. I actually read through all of Passengers and thought it was great!, but never fully read all of Shadow-19...
Today, after reading the news on here about a blogger revealing that AH was actually real, I went through those two early Spaihts scripts again and check out what I stumbled upon on page 20 of Shadow-19:
Prometheus is half a kilometer across, with a mass of seventy
million tons. And history's biggest gravity drive running through its
core. It’s a magnificent monster.
Prometheus has no passenger compartments, no cockpit.
It's a super-intelligent machine designed to transform Erix into a
A terraforming ship.
So is Ridley and Lindelof's new 'Prometheus' movie based on this other idea from one of Jon Spaihts early scripts?! Seems to fit perfectly with all the facts so far. Might stay up late tonight and read Shadow-19 more closely now!
A copy of the download link for Shadow-19: http://pdfcast.org/pdf/shadow19