About the stock truck 12-bolt, it's rare that I hear about breakage, especially with street tires and auto trans. $2K to replace the R+P in your 12-bolt does seem high to me. For that much I would expect high quality gears and all new bearings, along with dinner and drinks for two!
If the price is just for labor, that seems really high, seeing as how I have done it in my garage, on my back in around 8-10 hours. A pro with a lift should be able to knock it out in half that time. And he'd better be a pro, with lots of R+P swaps under his belt.
As for the 9-inch from Speedway, is it complete--axle flange to axle flange--and designed to bolt right into your truck? Also, how much torque is it designed to handle? Is it a stock Ford case, stronger nodular iron case, or what?
You should also check with Currie and Strange.
Edit: Is your engine a big block? What displacement? 600-700hp at the crank is massive, at least in my world.
Can the trans handle that much?