is the step through frame a deal breaker? if it's not you could buy all these parts from nashbar and build the bike from scratch for about $500 if you have mechanical skills. if you have to take it to a shop to do assembly it could run you a couple hundred more. Plain nashbar frames are $100 and a carbon fork is also $100. Cheap set of wheels from them is also about $100, cheap mtb crank can be had there as well. I agree that if your going to buy a whole bike, your probably gonna want to find something that has as much of what you want to begin with. there are tons of hybrids on the market that come with a MTB crank to begin with so that shouldn't be too hard but often times they have suspension forks. Part of the problem with costs is typically these kind of bikes have low end parts so you won't recoup much in trying to sell of the stuff your remove.
I don't think your idea is totally crazy, I spent close to $1000 for my custom build from nashbar because I really wanted a few specific features like a carbon fork AND disc brake. I paid a little more but i have exactly what I want. Cost is what you pay, value is what you get!