hondata just released flash pro for 09-10. so you might have to wait till they tweak it for 11-12.
bunch of intake's out there. injen, ct-icebox, takdeda, aem, etc
our headers are a cast in header, so not much you can do. you can try a RBC/RRC manifold instead.
exhaust - only one available in the state is the ct exhaust. otherwise you gonna have to import from japan or russia or germany. go with a custom one, it'll probably be cheaper and better.