There are a few common causes which seem to produce the idle problems in these trucks.
1) Intake leak (somewhere) which causes surging also.
2) PCV valve (back of motor) loose causes rough idle and stalling.
Is your Check engine light on?? is it functional?

as for the power loss, the headers can cause a tq loss. We ended up adding alot of timing to make up the tq I originally loss in my truck after the exhaust modification.

You have alot of chip options, but truthfully you need to find a local tuner to you and have the truck dyno tuned for optimal results. A standard chip is set to to modify settings for a stock truck, the custom tune wil take into consideration your modifications.