IMHO you ought to just save your money for now.
The Scorpion seems to be limited by air, fuel and strength. From what I've read, every compound turbo setup has windowed the block.
Granted some are blaming tunes on this, but still, pretty scary when rods are failing at 500-600hp. Ford was touting forged rods in one advertisement I saw. Other reports are the rods are powdered metal.
So, to 'get crazy' with power, at minimum you need turbos, fuel upgrades, stronger rods. And that's what we know about today.
There's several groups/individuals who are working on getting more power from the 6.7, but for now, the only recipe that's proven is a simple tuner. The rest are blowing engines. And the tuned ones are eating turbos - turbo overspeed.
Or, if your pockets are deep enough, join the compound groups and take pictures of all the pretty windows it puts in your engine. Always like to see carnage photos.
As to dropping in a manual. I think this is going to be virtually impossible. The computer is not made to work with a manual trans so even if you get one in there the computer is going to hate not having an automatic to talk to.
2012 F350, 6.7L Diesel, 4x4, SRW, Crew Cab, Short Box, Loaded, Ingot Silver
Detroit Truetrac, Icon leveling springs, steering damper mounts, King reservoir shocks and steering damper, Ultra Predator 22x10 and Nitto Terra 325/50R22 (35"s), H&S Minimaxx & Gearhead, aFe 5" SS w/ muffler, Leer XL, LineX, Titan 50gal, Airlift bags and wireless.