If you're a mechanically inclined, have tools, jack, welder or access to one, and some patience you can do the 5MT install, for much much less then 3k if you pull the parts yourself.
Agree that manual is the way to go. I've driven both and the stick is a blast!. If you're paying for someone else to do it, I'd drop the extra cash for the 5MT. Nothing like dropping the shifter into 4th at 65mph and feeling the SVX smoothly glide past others. I will never go back to the Auto for my daily driving. I feel totally connected to the car. And the 3.3 sounds bad a$$ at 4000rpm. My experience is, you can drive a manual trans until the wheels fall. I've yet to see an Auto outlast a Manual trans, which means longevity, with less headache, for the SVX.
Good luck!
P.S. You can get an idea on what 5MT parts might cost at a regular auto salvage yard from
http://car-part.com Keep in mind all prices are negotiable so multiply all parts by 70% and you'll have a good estimate.