Quite a project! Sounds like you need a program like Showmagic. I work with projection quite often with bands in theatres, but not to the same kind of degree of detail that you want. I usually just use one projector onto a 40ft screen as a backdrop, synced to the bands click track.
I think your only option will be to render the areas of image into separate video streams and play them as standalone videofiles. For example. x1,y1,x2,y2 and render as it's own file x 8, giving you 8 different videos. Showmagic runs this kind of set-up in theatres in the West end etc and I think also do Pink Floyds projection set up when they're on tour. It sends different streams to different projectors frame syncronised (accuracy 1/25th second). The version I use is Showmagic 512. I think you should give Kevin a call and talk to him. PM me for the number or google Showmagic. Be prepared to pay though. It's not cheap.
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