Oh, yeah, it would be astronomical to spend the THOUSANDS of dollars to change the car from auto to manual tranny. The main problem is that the car is built to house the auto mechanism, especially where it comes into the driver section. A manual has completely different linkage setup.
Changing trannies out like this is always a desire for lots of people. But it is MUCH better to just keep looking for same car in manual standard. I can't even consider how many thousands of dollars it would seriously cost to change it over. If you're a big shot car designer and have hundreds of thou' to spend, then go for it. But a normal person just trying to get a good fun car, don't bother.
Just keep looking, you'll find a Mustang manual that will suit you much better. I know how sad that can be, especially when a specific car has caught your eye. You just don't want to let it go, and you'll consider almost anything to get it. Sorry.