Since I am impatient and I cannot find a single Fender Custom Shop Fat 50 for the neck on eBay or Musicians Friend, I am thinking about getting one that is for the bridge position and putting it in the neck of my strat.

Would I be shortchanging my self in the David Gilmour set up I am doing on my strat? How much different would the sound be? Is it just a silly idea in the first place and should I just be more patient?

How much different is the Fender CS Fat 50 neck from the Fender CS Fat 50 bridge?
This set has the neck pickup in it. Course $250 for a set, that's ridiculous, Fender pickups aren't even that good. http://www.fender.com/products/search.php?partno=0992113000

I would look into Barenuckle pickups, you can pickup a full set of single coils that are much better for the same price.

And to answer your question, the neck is the lowest output pickup in the set, so technically, no, you wont get the same tone from putting the bridge pickup in the neck, if you do that the neck will prolly be slightly bassy and louder than the other pickups.