a $1000? A side?!?!
wow, that's crazy. Does that at least include the parts?
As far as the tuner, you don't need dyno time unless you are getting a full custom tune. I know the SCT handhelds are well under $400 and their boxed tunes will do just fine unless you have something beyond just the basic bolt ons. And let you set your shift points yourself.
While I cannot attest to it personally, my understanding is that a set of shorty headers would fall into the basic bolt on category, but if you were going with a set of full length headers and a very hugh flow dual exhaust, then a custom tune would be in order. But unless you have some other serious engine and fuel mods you'd probably be hurting your power (specifically torque) more than you would be helping.
Just my 2¢