One option is to build a low deck engine. A low deck Mopar is still taller than a Chevy big block so it isn't really all that low of a deck but it will give you more room under the hood. If you are going to step up to a 540 or 572 with an aftermarket block you can build either one in an Indy block. At least take a look at the option and see what the cost would be. There is only a couple of Indy intakes for the low block so that is a limitation.

You might come to the conclusion that a custom hood will save you money in the long run. If the goal is 900 hp you'll need a lot good parts. Handicapping yourself with a flat hood makes the job a lot harder.

Other option is to supercharge your existing engine. A centrifugal blower can be hung off the front of the engine and then you can tune the power by changing the pulley ratio. That setup will fit under your hood and give you all the power you need. A front facing intake manifold with a big throttle body will clear a stock hood.

The headers are going to be an issue. You might end up needing custom 2 inch headers to make your power goals. 2 inch headers will support 900 hp but most people would go even larger.