This is rare air, building a motor like this, at least for me! My guess is toss around the idea of a PSO head,B1TS,or Brewers, testing to find out the minimum bore size for no valve shrouding. Then run more stroke to keep the piston dome size down. Over size roller bearing cam, Pistons, rings etc picked by the best power producer in the engine building world that you can find. Dry sump, high vacuum, every trick you can do to a crank to reduce windage. You will wind up with a rod of almost 7.10 length, rod ratio of 2.25 or so. I don't know how that will affect things, but it will have to be looked at. An after market block may have the deck thickness to reduce the deck height quite a bit. If you are certain you will try using a stock block, then a center counter weighted crank will help.
Basically, I would be looking for an engine builder with experience in high Hp comp classes, or pro stock. They would be able to sort through this stuff and figure out an engine program that will meet the goals.
I don't see a problem making 1000+ hp, just how fat the wallet is. This stuff is real high $$.