Lonegunman is correct, you'll get KILLED in labor cost...because they're not JUST swapping the transmission, they're adding/replacing a plethora of other components.
I wouldn't even consider a swap like that...its a waste of money unless you plan to keep the car for a long time, because you're devaluing it.
An automatic transmission (as you know) is more expensive to purchase...and the car would be worth much less to a dealer when trading it in once they learn (via the VIN number) that the car has been altered from its original configuration...because it will be harder for them to sell. If you sell the car to an individual, it may not be a problem...but I wouldn't buy a car that had been altered like this unless it was a SMOKIN deal and the work was done by someone I knew by reputation!!
Take the cash and put it on a down payment for a new '05 with a factory manual transmission!! Or get yourself a low mileage pre-owned Mustang...I'm sure there will be more than a few people who want to trade up to the new body style, or you might get a really good deal on an '04 if they have one left with a manual
tranny...I know I did!!
Just my humble opinion.